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Protein tuzilishi parametrlari

Protein tuzilishi parametrlari


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Men oqsil tuzilishini aniqlash uchun zarur bo'lgan minimal parametrlar to'plami haqida qiziqaman. Mening tushunganim shundaki, magistralning geometriyasi phi va psi burchaklari (burilish burchaklari) bilan belgilanadi va keyin ushbu shablondan yon zanjirli rotamerlar aniqlanadi. Bu geometrik tuzilmani yaratish uchun etarlimi yoki boshqa omillar ham bormi?

Tegishli eslatmada, ikkita protein tuzilishi aniq qanday taqqoslanadi? Men ko'pincha foiz o'xshashligi haqidagi havolalarni ko'raman, lekin bu aslida nimani anglatadi? Protein ma'lumotlar bankida atom koordinatalari berilgan, ammo mening sezgiim shundaki, koordinatalar faqat zanjirdagi barcha boshqa aminokislotalarga nisbatan muhimdir. Boshqacha qilib aytganda, mutlaq koordinatalarni taqqoslash ma'lumotga ega bo'lmagan ko'rinadi.


Bu tavsif qanchalik aniq bo'lishini xohlayotganingizga bog'liq. Ideal bog'lanish uzunligi odatda qabul qilinadi, shuning uchun strukturani ph, ps, ʼn (umurtqa suyagi uchun) va ch1-c5 (yon zanjir uchun) burchaklar yordamida tasvirlash mumkin. Bu ko'p hollarda qo'llaniladigan narsa. Biroq, yon zanjirlardagi vodorodlarning pozitsiyalari ushbu tavsif bilan aniq belgilanmagan. Bu shuningdek, vodorod aloqalari va disulfid ko'priklarini tasvirlamaydi, ammo ularni nisbiy pozitsiyalardan chiqarish mumkin.

Qo'shimcha ma'lumotni bu yerda olishingiz mumkin: http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.1b.html

Ushbu tavsif ko'pchilik ilovalar uchun etarli bo'lishi kerak.


Protein tuzilmalarini solishtirish

Siz ko'rib chiqishingiz mumkin bo'lgan bir qator narsalar mavjud, masalan, o'rtacha kvadrat og'ish. Bu usul ikkita strukturaning koordinatalarini bir-birining ustiga qo'yish orqali taqqoslaydi.

  • RMSD: Bu Modeller modellashtirishda amalga oshiriladi yoki USCF Chimera-da foydalanish mumkin
    • RMSD angstrom kvadratidagi raqamni beradi, yuqori qiymatlar strukturaviy farqlarni ko'rsatadi. RMSD 0,0 bo'lsa, tuzilmalar bir xil ekanligini ko'rsatadi. C-alfa, magistral va butun atom kabi RMSD hisoblarining har xil turlari mavjud. C-alpha RMSD RMSDni hisoblash uchun faqat C-alfa atomlariga qaraydi. Magistral RMSD faqat magistralga qaraydi va RMSDni hisoblash uchun barcha atomlar barcha atomlarni hisobga oladi.

Ko'rib chiqiladigan boshqa narsalar

  • Tuzilmani o'zingiz yaratgan deb hisoblasangiz, struktura minimallashtirildimi? To'qnashuvlarni olib tashlash uchunmi?

  • Bundan tashqari, yuqorida aytib o'tilgan phi, psi burchaklari va siz tuzilmangizdagi to'qnashuvlarni tekshirdingizmi? To'qnashuvlarni USCF chimera-da tekshirish mumkin, u standart qiymati 0,6 Angstrom van der Wall radiusi o'xshashligini tekshiradi.


SWISS-MODEL: evolyutsion ma'lumotlardan foydalangan holda oqsilning uchinchi va to'rtlamchi tuzilishini modellashtirish

Marko Biasini, Stefan Bienert, Endryu Uoterxaus, Konstantin Arnold, Gabriel Studer, Tobias Shmidt, Florian Kiefer, Tiziano Gallo Kassarino, Martino Bertoni, Lorenza Bordoli, Torsten Shvede, Shveytsariya-MODEL: oqsilning uchinchi va to'rtlamchi ma'lumotlar tuzilishini evolit yordamida modellashtirish Nuklein kislotalarini tadqiq qilish, 42-jild, W1-son, 2014-yil 1-iyul, W252–W258 sahifalar, https://doi.org/10.1093/nar/gku340


Protein tuzilishi parametrlari - Biologiya

Cubic - bu Jorjiya universitetidagi Hisoblash tizimlari biologiyasi laboratoriyasi tomonidan ishlab chiqilgan vosita bo'lib, oqsillarni bog'lash joyini bashorat qilish uchun ishlatiladi. Cubic dastlab doktor Viktor Olman tomonidan ishlab chiqilgan, keyin esa doktor Jizhu Lu tomonidan yanada ishlab chiqilgan va optimallashtirilgan (bir protsessorli mashinalarda 10 baravar tezlashtirish). Cubic yuqori oqim ketma-ketliklarini va bir nechta boshqa parametrlarni kirish sifatida qabul qiladi va chiqish sifatida bog'lanish joylari to'plamini va ularning statistik ahamiyatini yaratadi.

JCUBIC - bu CUBIC dasturi uchun Java-ga asoslangan GUI bo'lib, u transkripsiya faktorini bog'lovchi saytni bashorat qilish uchun ishlatilishi mumkin.

JPOP (Joint Prediction of Operaons) dasturi JPOP operon tuzilmalarini bashorat qilishda yordam beradigan java dasturlari va Mathlab skriptlari to'plamidir. JPOP ketma-ket genomdagi operon tuzilmalarini bashorat qilish uchun genomik ma'lumotlarning uchta manbasini birlashtiradi:

Yopiq manba loyihalari Quyidagi paketlardan birini yuklab olish orqali siz Afinadagi Jorjiya universitetining Oak Ridge National Labs (ORNL) va Computational System Biology Lab (CSBL) tomonidan himoyalangan dasturlardan faqat tadqiqot maqsadlarida foydalanishga rozilik bildirasiz. Siz ushbu dasturni boshqa laboratoriyalarga o'tkazmaysiz yoki qayta tarqatmaysiz. Himoyalangan dasturiy ta'minot yordamida olingan har qanday ommaviy hisobot yoki natijalarni nashr etish tegishli iqtibos bilan foydalanishni tan olishiga rozilik bildirasiz.
Ushbu litsenziya CSBL tomonidan chiqarilgan ochiq kodli dasturiy ta'minotni qamrab olmaydi yoki qo'llamaydi.

Onlayn qo'llanma

Butun paketni prospect

Qismlar bo'yicha istiqbol:

Prospect bin papkasi prospect_bin.tar.gz (2 Megs)
MacosX papkasi prospect_bin_macosx.tar.gz (4 Megs) uchun istiqbolli quti
Prospect ma'lumotlar papkasi prospect_data.tar.gz (94 Megs)


Agar siz PROSPECT dan foydalansangiz, quyidagi manzilga murojaat qiling:

Agar siz Domainparser2 dan foydalansangiz, quyidagi manzilga murojaat qiling:

Onlayn qo'llanma

Platforma Java VM ni o'z ichiga oladi Java VM holda Buyruqlar qatori bajariladi
Kompyuter (Windows) Yuklab olish (7344K) Yuklab olish (1492K) Yuklab olish (120K)
Solaris Yuklab olish (7684K) Yuklab olish (1312K) Yuklab olish (72K)
Linux Yuklab olish (7684K) Yuklab olish (1312K) Yuklab olish (72K)
DEC Alpha Yuklab olish (7692K) Yuklab olish (1320K) Yuklab olish (116K)

Eslatma: Interfeys paketlari (jumladan, Java VM yoki Java VMsiz) buyruq qatori bajariladigan fayllarni o'z ichiga oladi.

Agar siz EKSKAVATORdan foydalansangiz, quyidagi manzilga murojaat qiling:

Qu Y, Guo JT, Olman V, Xu Y. (2004) siyrak dipolyar ulanish ma'lumotlaridan foydalangan holda oqsil tuzilishini bashorat qilish. Nuklein kislotalari Res.,32, 551-561.

Y. Qu, J.-T. Guo, V. Olman va Y. Xu, Qoldiq dipolyar ulanish ma'lumotlarini qo'llash orqali oqsil qatlamlarini aniqlash, Biokompyuter bo'yicha Tinch okeani simpoziumi, 2004, 459-470.


Protein tuzilishi parametrlari - Biologiya

Sizga kerak bo'lgan yagona narsa (oqsil tuzilishini bashorat qilish uchun)

Ushbu loyiha to'liq (barcha atom) oqsil tuzilishini bashorat qilish uchun ketma-ketlikni modellashtirish usullarini o'rganadi. Ish tilni modellashtirish metodologiyalaridan ilhomlangan va shuning uchun Transformer va diqqatga asoslangan modellarni o'z ichiga oladi. Muhimi, bu ham davom etayotgan ish va faol tadqiqot loyihasidir. Men har qanday fikr yoki qiziqishni qabul qilaman!

Agar siz atrofga nazar tashlamoqchi bo'lsangiz, ushbu paketga tegishli barcha kodlarni protein_transformer katalogida topish mumkin. train.py modellarni yuklaydi va o'tkazadi, modellar modellarda aniqlangan/ , va proteindagi kod/ oqsil tuzilishi va ketma-ketlik ma'lumotlarini manipulyatsiya qilish va yaratish uchun javobgardir. Ko'pgina boshqa tadqiqot hujjatlari hozirda tadqiqotga kiritilgan/ , lekin skriptni ishga tushirish uchun kerak emas.

Og'irliklar va tarafkashliklar bilan integratsiyalashuv tufayli siz model mashg'ulotingiz holatini Og'irliklar va tarafkashliklar boshqaruv panelida (quyida) osongina kuzatishingiz mumkin. Ko'pgina o'quv statistikasi real vaqt rejimida, shu jumladan har bir bashoratning 3D tuzilishi qayd etiladi.

Ushbu kodni ishga tushirish uchun, avvalambor, pip install -e bilan joriy muhitingizda pip bilan paketni ishlab chiquvchi o'rnatishni amalga oshirish tavsiya etiladi. . Bu sizning muhitingizga protein_transformer paketini o'rnatadi va agar xohlasangiz, o'zingizning o'quv skriptingizga har qanday sinf yoki pastki dasturlarni bepul import qilishingiz mumkin.

  • ProDy
  • Pytorch
  • numpy
  • scipy
  • tqdm
  • collada2gltf (conda install -c schrodinger collada2gltf)

Muvaffaqiyatli o'rnatishdan so'ng, protein_transformer katalogiga o'ting, u erda tren.py bilan modelni o'rgatishingiz mumkin.

Iltimos, train.py-dagi har qanday tayoqchani ishga tushirish sozlamalarini o'zgartiring, shunda ular meniki emas, balki sizning tayoqcha loyihangizga ishora qiladi :)

Ushbu skript turli xil arxitektura va trening sozlamalarini aniqlash uchun juda ko'p turli xil dalillarni oladi.

Hozirda qo'llab-quvvatlanadigan modellar transformatorning "Faqat kodlovchi" versiyasiga asoslangan va ularga -m argumentlari bilan kirish mumkin. . enc-dec hozirda eskirgan.

Trening ma'lumotlari Muhammad AlQurayshining ProteinNet tarmog'iga asoslangan. Ushbu loyiha bilan ishlash uchun o'zgartirilgan CASP12 tanlovidan oldindan ishlangan ma'lumotlarni bu yerdan yuklab olish mumkin (

3 GB, ma'lumotlar to'plamining 30% yupqalashi).

Mening ma'lumotlarim ProteinNet bilan bir xil poezd/test/tasdiqlash to'plamlaridan foydalanadi. ProteinNet singari, u oqsil ketma-ketligi va koordinatalarini o'z ichiga olgan bo'lsa-da, men uni butun protein tuzilishi (umurtqa va yon zanjir atomlari) haqidagi ma'lumotlarni o'z ichiga olgan holda o'zgartirdim. Shunday qilib, ma'lumotlar to'plamidagi har bir oqsil ketma-ketlik, ichki burilish / bog'lanish burchaklari va koordinatalar uchun ma'lumotlarni o'z ichiga oladi. U bir nechta ketma-ketlikni tekislash yoki ikkilamchi tuzilish izohini o'z ichiga olmaydi.

Ma'lumotlar PyTorch bilan saqlanadi va Python lug'atida shunday saqlanadi:

Iltimos, loyiha haqida ko'proq ma'lumot olish uchun mening loyiha eslatmalariga tashrif buyuring.

Bu ombor dastlab https://github.com/jadore801120/attention-is-all-you-need-pytorch dan vilka edi, lekin o'shandan beri men qulayroq bo'lganim uchun ushbu maxsus loyiha ehtiyojlariga mos ravishda qayta yozildi. Pytorch, Transformers va boshqalar bilan. Ramka uchun jadore801120 uchun katta rahmat.

Men, Jonatan King, HHMI-NIBIB Interfaces Initiative dasturining bir qismi sifatida NIH T32 o‘quv granti T32 EB009403 tomonidan qo‘llab-quvvatlanadigan doktorlik stajyoriman.

Loyiha tuzilmasi (doimiy integratsiya, hujjatlar, testlar) Python Cookiecutter 1.1-versiyasi hisoblash molekulyar faniga asoslangan.


Biokimyo


T-hujayra retseptorida mavjud bo'lgan biokimyoviy tuzilmalarni ko'rsatadigan rasm (Mishel Mishke rasmi).

Ushbu bo'lim kursni tanishtiradi va biokimyo va hujayra tarkibi asoslarini qamrab oladi. Birinchidan, biz hayotning tashkiliy darajalari va organizmlarning har xil turlari bilan tanishamiz. Keyin biz biologik molekulalarning tuzilishi va bu molekulalarning hosil bo'lishida ishtirok etadigan molekulyar kuchlarni ko'rib chiqamiz. Biz lipidlar, uglevodlar va nuklein kislotalarning umumiy tuzilishi va funktsiyalari, shuningdek, oqsillarning tarkibi, tuzilishi va funktsiyalari bilan tanishamiz. Makromolekulaning asosiy guruhlari bilan tanishganimizdan so'ng, biz metabolizmdan, Gibbsning erkin energiyasidan, biokimyoviy reaktsiyalardan, fermentlardan va energiya valyutasi sifatida ATPdan boshlab, ularning hujayra ichidagi o'zaro ta'sirini o'rganamiz. Biz glyukoza va unga aloqador shakarlardan energiya yig'ishning hujayra mexanizmlarini ko'rsatamiz, ATP hosil qilish mexanizmi sifatida glikolizni qisqacha bayon qilamiz va anaerob va aerob sharoitlarda glikolizda hosil bo'lgan piruvat taqdirini muhokama qilamiz. Va nihoyat, biz tsiklik va siklik bo'lmagan fotofosforillanishning umumiy g'oyalarini va bu ikki jarayon hujayralar tomonidan fotosintezda Kalvin tsikli uchun zarur bo'lgan ATP va NADPH ni yaratish uchun qanday ishlatilishini ko'rib chiqamiz.

Ushbu bo'lim davomida siz hujayraning kimyoviy va molekulyar tarkibini tasvirlab berasiz va biologik makromolekulalarning asosiy tarkibiy qismlarini aniqlaysiz. Siz biologik tizimlarda harakat qiluvchi kuchlarni aniqlaysiz: kovalent aloqalar, ion aloqalari, vodorod aloqalari, Van der Vaal kuchlari va hidrofobiklik. Siz umumiy aminokislotalarni chizasiz va yon zanjirning tabiatiga qarab 20 ta aminokislotaning har birini mos ravishda toifalarga ajratasiz. Termodinamikaning umumiy qonunlarini biologik reaksiyalarga ham qo'llaysiz. Bundan tashqari, siz Gibbsning erkin energiyasini aniqlaysiz, biokimyoviy reaktsiya bilan bog'liq Gibbs erkin energiya o'zgarishini aniqlaysiz va o'z-o'zidan paydo bo'ladigan va o'z-o'zidan bo'lmagan reaktsiyalarni aniqlaysiz.

Ushbu bo'lim oxirida siz hayotni tashkil etishning turli darajalari va eukaryotik va prokaryotik hujayralar o'rtasidagi farqlar bilan tanishasiz. Siz makromolekulalarning asosiy guruhlari, jumladan lipidlar va fosfolipidlar, uglevodlar nuklein kislotalari va oqsillarning tuzilishi va xususiyatlarini, shuningdek ularning hujayradagi funktsiyalarini tushunasiz. Siz oqsil tuzilishining birlamchi, ikkilamchi, uchinchi va to'rtlamchi darajalari bilan tanishasiz va har bir darajani qanday turdagi bog'lanishlar va kuchlar barqarorlashtirishini bilasiz. Bundan tashqari, siz aminokislotalarni almashtirishning oqsilning umumiy tuzilishi va funktsiyasiga ta'sirini tushunasiz. Siz ATP qanday qilib uyali ish uchun energiya berishini bilib olasiz.

Va nihoyat, siz hujayrali nafas olish va fotosintezdagi reaktsiyalar, ular qachon paydo bo'lishi va nima uchun muhimligini ko'proq tushunasiz. Siz hujayrali nafas olish va fotosintez o'rtasidagi munosabatlarni tushunasiz.

Ushbu kursda aniq narsani qidiryapsizmi? Resurslar indeksi ko'pgina kurs resurslariga havolalarni bitta sahifada to'playdi.


RCSB PDB haqida: Ilmiy va biotibbiyot tadqiqotlari va ta'lim sohasidagi yutuqlarni qo'llab-quvvatlash

Protein ma'lumotlar banki (PDB) barcha biologiya va tibbiyotda birinchi ochiq kirish raqamli ma'lumotlar resursi sifatida tashkil etilgan (Tarixiy Xronologiya). Bugungi kunda u ilmiy kashfiyotlar uchun markaziy eksperimental ma'lumotlar uchun etakchi global resurs hisoblanadi.

Internet-axborot portali va yuklab olinadigan ma'lumotlar arxivi orqali PDB yirik biologik molekulalar (oqsillar, DNK va RNK) uchun 3D tuzilish ma'lumotlariga kirishni ta'minlaydi. Bular sayyoradagi barcha organizmlarda uchraydigan hayot molekulalari.

Biologik makromolekulaning 3D tuzilishini bilish uning inson va hayvonlar salomatligi va kasalliklaridagi rolini, o‘simliklardagi, oziq-ovqat va energiya ishlab chiqarishdagi funksiyasini hamda global farovonlik va barqarorlik bilan bog‘liq boshqa mavzulardagi ahamiyatini tushunish uchun zarurdir.

RCSB PDB (Tuzilishviy bioinformatika PDB tadqiqot hamkorligi) global PDB arxivi uchun AQSh ma'lumotlar markazini boshqaradi va PDB ma'lumotlarini foydalanishda cheklovlarsiz barcha ma'lumotlar iste'molchilariga bepul taqdim etadi (Siyosatlar).

Strukturaviy biologiya, hujayra va molekulyar biologiya, hisoblash biologiyasi, axborot texnologiyalari va ta'lim sohalarida taniqli mutaxassislar RCSB PDB maslahatchilari sifatida xizmat qiladi.


Protein tuzilishi parametrlari - Biologiya

Pfam ma'lumotlar bazasi protein oilalarining katta to'plami bo'lib, ularning har biri vakili bir nechta ketma-ketlikni tekislash va yashirin Markov modellari (HMMs). Ko'proq.

Proteinlar odatda bir yoki bir nechta funktsional hududlardan iborat bo'lib, ular odatda deyiladi domenlar. Domenlarning turli xil birikmalari tabiatda mavjud bo'lgan turli xil oqsillarni keltirib chiqaradi. Proteinlar ichida paydo bo'ladigan domenlarni identifikatsiya qilish, shuning uchun ularning funktsiyalari haqida tushuncha berishi mumkin.

Pfam shuningdek, deb nomlanuvchi tegishli yozuvlarning yuqori darajadagi guruhlarini yaratadi klanlar. Klan - bu ketma-ketlik, tuzilish yoki profil-HMM o'xshashligi bilan bog'liq bo'lgan Pfam yozuvlari to'plami.

Har bir kirish uchun taqdim etilgan ma'lumotlar UniProt Reference Proteomlariga asoslanadi, ammo alohida UniProtKB ketma-ketliklari haqidagi ma'lumotni hali ham protein qo'shilishi orqali topish mumkin. Pfam to'la Turli xil ulanishlarni (masalan, barcha UniProt va NCBI GI) yoki turli darajadagi zaxiralarni ta'minlash uchun turli xil ma'lumotlar bazalarini qidirish orqali tekislash mumkin.

  • TEZKOR havolalar
  • TARTIBIY QIDIRISH
  • PFAM YAZISHINI KO‘RISH
  • KLANNI KO'RISH
  • BIRINCHILIKNI KO'RISH
  • TUZILMANI KO'RISH
  • KALİT SO'ZLARNI QIDIRISh
  • O'TGAN

Pfam-da ma'lumotlarni turli yo'llar bilan topishingiz mumkin.

  • Pfam o'yinlari uchun protein ketma-ketligini tahlil qiling
  • Pfam izohlari va hizalamalarini ko‘ring
  • Tegishli yozuvlar guruhlarini ko'ring
  • Protein ketma-ketligining domen tashkilotiga qarang
  • PDB strukturasidagi domenlarni toping
  • Kalit so'zlar bo'yicha Pfam so'rovi
  • Yoki qo'shimcha ma'lumot olish uchun yordam sahifalarini ko'ring

Pfam o'yinlari uchun protein ketma-ketligini tahlil qiling

Tegishli Pfam yozuvlarini topish uchun protein ketma-ketligini bu yerga qo'ying.

Bu qidiruv va E-qiymati 1.0 dan foydalanadi. Bu yerda siz oʻzingizning qidiruv parametrlaringizni oʻrnatishingiz va bir qator boshqa qidiruvlarni amalga oshirishingiz mumkin.

Pfam izohlari va hizalamalarini ko‘ring

Yozuv identifikatorini kiriting (masalan, Piwi) yoki qo'shilish (masalan, PF02171) ushbu yozuv uchun barcha ma'lumotlarni ko'rish uchun.

Qarindosh oilalar guruhlarini ko'ring

Klan identifikatorini kiriting (masalan, Kazal) yoki qo'shilish (masalan, CL0005) oʻsha klan haqidagi maʼlumotlarni koʻrish uchun.

Protein ketma-ketligining domen tashkilotini ko'rish

Ketma-ket identifikatorni kiriting (masalan, VAV_INSON) yoki qo'shilish (masalan, P15498).

PDB strukturasidagi domenlarni toping

PDB identifikatorini kiriting (masalan, 2abl) Protein ma'lumotlar bankidagi tuzilma uchun.

Kalit so'z bo'yicha Pfam so'rovi

Pfam ma'lumotlar bazasida matn ma'lumotlarida kalit so'zlarni qidiring.


Tuzilishi va funktsiyasi

Talabalar makromolekulyar tuzilish va funktsiyaning asosiy tushunchalarini, shu jumladan biologik makromolekulalarning tabiatini, ularning suv bilan o'zaro ta'sirini, tuzilishi va funktsiyasining o'zaro bog'liqligini, tez -tez uchraydigan mexanizmlarini tushuntirish va qo'llay olishlari kerak.

Quyidagi o'quv maqsadlari kirish A, oraliq B va yuqori C deb tasniflanadi.

1. Biologik makromolekulalar katta va murakkab

Makromolekulalar asosiy molekulyar birliklardan iborat. Ularga oqsillar (aminokislotalarning polimerlari), nuklein kislotalar (nukleotidlar polimerlari), uglevodlar (shakar polimerlari) va lipidlar (turli xil modulli tarkibiy qismlar) kiradi. Biologik makromolekulalarning biosintezi va degradatsiyasi chiziqli polimerizatsiyani, parchalanish bosqichlarini (oqsillar, nuklein kislotalar va lipidlar) o'z ichiga oladi, shuningdek tarmoqlanish/debranshni (uglevodlar) o'z ichiga olishi mumkin. Bu jarayonlar murakkab tartibga solinadigan ko'p oqsilli komplekslarni (masalan, ribosoma, proteazoma) o'z ichiga olishi mumkin.

Bog'langan ta'lim maqsadlari

  • Talabalar turli xil biologik ahamiyatga ega makromolekulalar va makromolekulyar birikmalarning xilma-xilligi va murakkabligini evolyutsion moslik nuqtai nazaridan muhokama qila olishlari kerak. A
  • Talabalar makromolekulalarning asosiy birliklari va ular orasidagi bog’lanish turlarini tasvirlay olishlari kerak. A
  • Talabalar makromolekulalarning asosiy turlarini (oqsillar, nuklein kislotalar va uglevodlar) biosintezida ishtirok etadigan jarayonlarni solishtirib, farq qila olishlari kerak. B
  • Talabalar makromolekulalarning asosiy turlarini (oqsillar, nuklein kislotalar va uglevodlar. B) parchalanish jarayonlarini solishtirish va taqqoslash imkoniyatiga ega bo'lishlari kerak.
  • Talabalar oqsillar domenlardan iborat ekanligini tushunishlari va oqsil oilalari qanday qilib birlamchi genning ko'payishi natijasida paydo bo'lishini muhokama qilishlari kerak. C

2. Tarkibi bir necha omillar bilan belgilanadi

Kovalent va kovalent bo'lmagan bog'lanish oqsillar va nuklein kislotalarning uch o'lchovli tuzilmalarini boshqaradi, bu funktsiyaga ta'sir qiladi. Tabiatda kuzatilgan aminokislotalarning ketma-ketligi biologik funksiya uchun juda tanlangan, ammo o'ziga xos katlamli tuzilishga ega bo'lishi shart emas. Makromolekulalar tuzilishi (va shuning uchun funktsiyasi) kimyoning asosiy tamoyillari bilan tartibga solinadi, masalan: kovalent aloqalar va qutblar, bog'larning aylanishi va tebranishlari, kovalent bo'lmagan o'zaro ta'sirlar, molekulyar strukturaning hidrofobik ta'siri va dinamik jihatlari. Proteinlar va nuklein kislotalarning ketma -ketligi (va shuning uchun tuzilishi va funktsiyasi) muqobil biriktirish, mutatsiya yoki kimyoviy modifikatsiya orqali o'zgarishi mumkin. Makromolekulalar ketma-ketligi (shuning uchun tuzilishi va funktsiyasi) o'zgartirilgan yoki yangi biologik faollikni yaratish uchun rivojlanishi mumkin.

Bog'langan ta'lim maqsadlari

  • Talabalar biologik makromolekulalardagi takrorlanuvchi birliklarni taniy olishlari va kovalent va kovalent bo'lmagan o'zaro ta'sirlarning tarkibiy ta'sirini muhokama qilishlari kerak. A
  • Talabalar organizmlarda uchraydigan har xil turdagi biologik makromolekulalarning tarkibi, evolyutsion o'zgarishi va shuning uchun strukturaviy xilma -xilligini muhokama qilishlari kerak. A
  • Talabalar makromolekulalar tarkibi va tuzilishi o'rtasidagi kimyoviy va fizik munosabatlarni muhokama qila olishlari kerak. A
  • Talabalar oqsil va nuklein kislotalarning birlamchi, ikkilamchi, uchlamchi va to'rtinchi tuzilmalarini solishtirib, farq qila olishlari kerak. B
  • Talabalar makromolekulyar boshlang'ich ketma -ketligi va tuzilishini tahlil qilish uchun turli xil bioinformatik yondashuvlardan foydalana olishlari kerak. B
  • Talabalar o'ziga xos aminokislotalarning kimyoviy modifikatsiyasining oqsilning uch o'lchovli tuzilishiga ta'sirini solishtirish va taqqoslash imkoniyatiga ega bo'lishlari kerak. B
  • Talabalar evolyutsion o'zgarishlar natijasida ma'lum bir makromolekulaning yangi funktsiyalarni bajarishi usullarini taqqoslashi va farqlashi kerak. B
  • Talabalar birlamchi ketma-ketliklarni solishtirish va saqlanish va/yoki evolyutsion oʻzgarishlarning makromolekulalar tuzilishi va funksiyasiga taʼsirini aniqlash uchun turli bioinformatika va hisoblash yondashuvlaridan foydalanishi kerak. C
  • Talabalar mutatsiyalarning oqsilning faolligiga, tuzilishiga yoki barqarorligiga ta'sirini bashorat qilishlari va mutatsiyalar ta'sirini baholash uchun tegishli tajribalar tuzishlari kerak. C
  • Talabalar biologik makromolekulalarning lokalizatsiyasi va o'zaro ta'sirini o'rganish uchun tegishli kimyoviy yoki kimyoviy biologik yondashuvlarni taklif qila olishlari kerak. C
  • Talabalar takrorlanadigan genning mutatsiyalari funktsional xilma -xillikni qanday yaratishini muhokama qilishlari kerak. C
  • Talabalar makromolekula tuzilishining tegishli darajalariga kimyoviy va energetik hissa qo'shishni baholay olishlari va strukturaning o'ziga xos o'zgarishlarining molekulaning dinamik xususiyatlariga ta'sirini bashorat qilishlari kerak. C

3. Tuzilishi va funksiyasi o‘zaro bog‘liq

Makromolekulalar boshqa molekulalar bilan har xil kovalent bo'lmagan o'zaro ta'sirlar yordamida o'zaro ta'sir qiladi. Ushbu o'zaro ta'sirlarning o'ziga xosligi va yaqinligi biologik funktsiya uchun juda muhimdir. Ba'zi makromolekulalar kimyoviy reaktsiyalarni katalizlaydi yoki fizik jarayonlarni (masalan, molekulyar transportni) osonlashtiradi, bu ularni atrof-muhit sharoitida davom ettirishga imkon beradi. Bu jarayonlar tezlik qonunlari va termodinamik printsiplar (masalan, to'qnashuv nazariyasi, o'tish holati nazariyasi, tezlik qonunlari va muvozanatlari, harorat va tuzilish va kimyoviy reaktivlikning ta'siri, Kulon qonuni, Nyutonning harakat qonunlari, energiya va barqarorlik, ishqalanish) bilan miqdoriy jihatdan tavsiflanishi mumkin. , diffuziya, termodinamika va tasodifiylik va ehtimollik tushunchasi).

Bog'langan ta'lim maqsadlari

  • Talabalar ma'lum bir reaktsiyani ferment yoki ribozim qanday katalizlashini tushuntirish uchun mexanik mulohazalardan foydalanishi kerak. A
  • Talabalar ferment mexanizmlarining har xil turlari uchun asoslarni muhokama qila olishlari kerak. A
  • Talabalar fermentativ stavkalarni hisoblashlari va bu stavkalarni solishtirishlari va bu stavkalarni uyali yoki organizmli gomeostaz bilan bog'lashlari kerak. B
  • Talabalar ligand-makromolekulalar kompleksining yaqinligi va stoxiometriyasini aniqlashda qo'llanilishi mumkin bo'lgan turli usullarni muhokama qilishlari va natijalarni termodinamik va kinetik ma'lumotlar bilan bog'lashlari kerak. B
  • Talabalar ligand-makromolekulalar majmuasida o'ziga xoslikka qo'shilgan hissalarni tanqidiy baholay olishlari va o'ziga xoslikka qo'shilgan hissalarni baholash uchun eksperimentlarni loyihalash va kompleksdagi ligand o'ziga xosligi haqidagi farazlarni sinab ko'rishlari kerak. C
  • Talabalar mutatsiya yoki ligand strukturaviy o'zgarishining bog'lanish yaqinligiga biologik va kimyoviy ta'sirini bashorat qilishlari va ularning bashoratlarini sinab ko'rish uchun tegishli tajribalarni ishlab chiqishlari kerak. C

4. Makromolekulyar o‘zaro ta’sirlar

Makromolekulalar va boshqa molekulalar o'rtasidagi o'zaro ta'sirlar makromolekulaning uch o'lchovli tuzilmalarini barqarorlashtirishda katta rol o'ynaydigan bir xil zaif, kovalent bo'lmagan o'zaro ta'sirlarga tayanadi. Hidrofobik ta'sir, ionli o'zaro ta'sirlar va vodorod bog'lanish o'zaro ta'siri sezilarli. Bog'lanish joyida yoki faol joyda o'zaro ta'sir qiluvchi kimyoviy guruhlarning tizimli tashkil etilishi bu o'zaro ta'sirlarga yuqori darajada o'ziga xoslik beradi. Ushbu o'zaro ta'sirlarning o'ziga xosligi va yaqinligi biologik funktsiya uchun juda muhimdir.

Bog'langan ta'lim maqsadlari

  • Talabalar o'ziga xoslik yoki yaqinlik o'zgarishlarining biologik funktsiyaga ta'sirini va har qanday potentsial evolyutsion ta'sirni muhokama qilishlari kerak. A
  • Talabalar ligand-makromolekulalar kompleksi uchun yaqinlik va stoxiometriyani aniqlash uchun ishlatilishi mumkin bo'lgan turli usullarni muhokama qilishlari va natijalarni termodinamik va kinetik ma'lumotlar bilan bog'lashlari kerak. B
  • Talabalar turli xil biologik molekulalar (jumladan, oqsillar, nuklein kislotalar, lipidlar, uglevodlar va mayda organik moddalar va boshqalar) o'rtasidagi o'zaro ta'sirlarni muhokama qilishlari va bu o'zaro ta'sirlar biologik funktsiyaning o'zgarishiga olib keladigan o'ziga xoslik yoki yaqinlikka qanday ta'sir qilishini tasvirlashlari kerak. B
  • Talabalar mutatsiya yoki ligand strukturaviy o'zgarishining bog'lanishning yaqinligiga ta'sirini bashorat qilishlari va ularning bashoratlarini sinab ko'rish uchun tegishli tajribalarni ishlab chiqishlari kerak. C
  • Talabalar denaturatsiya uchun zarur bo'lgan harorat (Tm) va makromolekulyar tuzilish o'rtasidagi bog'liqlikni muhokama qila olishlari kerak. C

5. Makromolekulyar tuzilma dinamikdir

Makromolekulyar struktura keng vaqt oralig'ida dinamikdir va katta va kichik dinamik tarkibiy o'zgarishlar ko'pincha biologik funktsiya uchun juda muhimdir. Kichik o'zgarishlar mahalliy molekulyar tebranishlar shaklida bo'lishi mumkin, bu kichik molekulalarning makromolekulaning ichki qismlariga kirishini osonlashtiradi. Katta konformatsion o'zgarishlar kataliz yoki boshqa ish shakllarini osonlashtirish uchun turli makromolekulyar domenlarning bir-biriga nisbatan harakati shaklida bo'lishi mumkin. Proteinlar o'z ichiga tuzilmagan domenlarni o'z ichiga olishi mumkin. Eritmada strukturaning yo'qligi bir nechta boshqa molekulalar bilan o'zaro ta'sirlar sodir bo'lishi kerak bo'lgan funktsiyani osonlashtirishi mumkin. Makromolekulyarlarning dinamik tuzilishi biokimyoviy va molekulyar biologik jarayonlarning gomeostazasiga ta'sir qiluvchi tez o'zgarishlarga imkon beradi.

Bog'langan ta'lim maqsadlari

  • Talabalar biologik makromolekulalar Adagi turli konformatsion ta'sirlarning vaqt shkalalarini muhokama qilishlari va konformatsiya va dinamikada ligandlar keltirib chiqaradigan o'zgarishlarni tekshirish uchun tegishli tajribalarni ishlab chiqishlari kerak. C
  • Talabalar makromolekulalar dinamik xususiyatlarining strukturaviy asoslarini muhokama qila olishlari va birlamchi ketma-ketlikning o'zgarishi natijasida paydo bo'lishi mumkin bo'lgan A dinamik xususiyatlarining o'zgarishi ta'sirini taxmin qilishlari kerak. C
  • Talabalar ketma-ketlikning tartibli yoki tartibsiz ekanligini oldindan aytib berishlari va oqsillarning tartibsiz hududlari uchun potentsial rollarni muhokama qilishlari kerak. B
  • Talabalar makromolekulyar funktsiyada dinamikaning rolini tasdiqlovchi va unga qarshi dalillarni tanqidiy muhokama qilishlari kerak. C

6. Makromolekulalarning biologik faolligi ko'pincha tartibga solinadi

Makromolekulyarlarning biologik faolligi ko'pincha bir yoki bir nechta ierarxik usullar bilan tartibga solinadi (masalan, inhibitorlar, aktivatorlar, modifikatorlar, sintez, degradatsiya va bo'linish).

Bog'langan ta'lim maqsadlari

  • Talabalar makromolekulaning yoki fermentativ reaktsiya yoki yo'lning funktsiyasini tartibga solishning turli mexanizmlarini solishtirish va taqqoslash imkoniyatiga ega bo'lishlari kerak. A
  • Talabalar reaksiyani allosterik tartibga solishning afzalliklari va kamchiliklarini muhokama qilishlari kerak. B
  • Talabalar allosterik regulyatsiya, kovalent regulyatsiya va makromolekulyar tuzilma-funktsiyaning gen darajasidagi o'zgarishlar misollarini muhokama qila olishlari kerak. B
  • Talabalar makromolekuladagi homotrop yoki heterotrop ligandlarga javoban tartibga solish turini baholash uchun eksperimental ma'lumotlardan foydalanishlari kerak. C
  • Talabalar makromolekulalar tuzilishi-funktsiyasining tartibga solinishini tushuntirish uchun modelni loyihalashtira olishlari kerak. C
  • Talabalar evolyutsiya makromolekulalar va jarayonlarni tartibga solishni qanday shakllantirganini tasvirlay olishlari kerak. C
  • Talabalar hujayra gomeostazidagi o'zgarishlar signalizatsiya va tartibga soluvchi molekulalarga va metabolik oraliq moddalarga qanday ta'sir qilishini tasvirlay olishlari kerak. C

7. Makromolekulalar tuzilishi (demak, funksiyasi) kimyo va fizikaning asosiy tamoyillari bilan tartibga solinadi.

Makromolekulalar tuzilishi (va shuning uchun funktsiyasi) kimyoning asosiy tamoyillari (shu jumladan kovalent aloqalar va qutbli bog'lanish aylanishlari va tebranishlar vodorod aloqalari va kovalent bo'lmagan o'zaro ta'sirlar, molekulyar strukturaning hidrofobik ta'sirining dinamik jihatlari to'qnashuv nazariyasi o'tish holati nazariyasi tezligi qonunlari va) bilan boshqariladi. harorat va tuzilish va kimyoviy reaktivlik ta'sirini muvozanatlash) va fizika (jumladan, Coulomb qonuni Nyuton qonunlari harakat energiyasi va barqarorlik ishqalanish diffuziya termodinamiği va tasodifiylik va ehtimollik tushunchasi).

Bog'langan ta'lim maqsadlari

  • Talabalar tezlik qonunlari va muvozanatning asosiy tamoyillarini reaktsiyalar va o'zaro ta'sirlar bilan bog'lashlari va reaktsiyalar va o'zaro ta'sirlar uchun tegishli termodinamik parametrlarni hisoblashlari kerak. A
  • Talabalar ligandning makromolekulaga ulanishi mumkin bo‘lgan eritmaga kiritilganda makromolekulaning qanday ta’sir qilishini tushuntira olishlari kerak. A
  • Talabalar asosiy tamoyillardan foydalanib, ferment katalizlangan reaksiyaga haroratning ta’sirini tushuntira olishlari kerak. B
  • Talabalar fizikaning asosiy tamoyillaridan foydalangan holda makromolekulaning dinamik xususiyatlarini muhokama qila olishlari kerak. B

8. Biologik makromolekulalarning tuzilishi, dinamikasi va funksiyasini kuzatish va miqdoriy jihatdan o‘lchash uchun turli eksperimental va hisoblash usullaridan foydalanish mumkin.

Biologik makromolekulalarning tuzilishi, dinamikasi va funksiyasini kuzatish va miqdoriy o‘lchash uchun turli eksperimental va hisoblash usullaridan foydalanish mumkin. Tenglamalar modellardan olinishi va natijalarni bashorat qilish yoki ma'lumotlarni tahlil qilish uchun ishlatilishi mumkin. Modelning to'g'riligini va ma'lumotlarning ishonchliligini baholash uchun ma'lumotlarni statistik tahlil qilish mumkin.


Membran oqsili haqida umumiy ma'lumot

Membran oqsillari tirik organizmlardagi oqsillarning uchdan bir qismini tashkil qiladi. Ularning tuzilishiga ko'ra membrana oqsillarining uchta asosiy turi mavjud: birinchisi - doimiy ravishda bog'langan yoki membrananing bir qismi bo'lgan integral membrana oqsili, ikkinchisi - lipid ikki qavatiga yoki boshqasiga vaqtincha biriktirilgan periferik membrana oqsili. integral oqsillar, uchinchisi esa lipid bilan biriktirilgan oqsillardir (1-rasm). Bu erda biz faqat membrana oqsilining dastlabki ikki turini tasvirlaymiz.

1-rasm Membrana oqsillarining strukturaviy tasnifi

Ikki qavat bilan aloqasiga ko'ra integral membrana oqsillarini ikkita asosiy turga bo'lish mumkin: integral politopik oqsillar va integral monotopik oqsillar. Integral politopik oqsillar “transmembran oqsillari” deb ham ataladi, ular membrana bo'ylab kamida bir marta o'tishi mumkin (2-rasm). Ushbu integral membrana oqsillari turli xil transmembran topologiyasiga ega bo'lishi mumkin, bu protein egallagan biologik membrananing ichki yoki tashqi tomonlariga nisbatan membranani qamrab oluvchi segmentlarning yo'nalishini (N- va C-terminallarning joylashishini) anglatadi. 2-rasmdagi dastlabki uchta tur integral membrana oqsillarida keng tarqalgan shakllardir, masalan, transmembran a-spiral oqsili, transmembran a-spiral oqsili va transmembran b-varaq oqsili.

Integral monotopik oqsillar integral membrana oqsillarining bir turi bo'lib, ular membrananing faqat bir tomoniga biriktirilgan va butun yo'l bo'ylab tarqalmaydi. Integral monotopik membrana oqsili va hujayra membranalari o'rtasida o'zaro ta'sirning 4 turi mavjud: amfipatika-spiral parallel, hidrofobik halqa, kovalent bog'langan membrana lipid va membrana lipidlari bilan elektrostatik yoki ionli o'zaro ta'sir (No4, 5, 6, 2-rasmning 7). Integral membrana oqsillarini biologik membranalardan faqat yuvish vositalari, qutbsiz erituvchilar yoki ba'zan denaturatsiya qiluvchi vositalar yordamida ajratish mumkin. Periferik oqsillar polar reagent bilan ishlov berishdan keyin ajralib chiqadi, masalan, pH darajasi yuqori yoki tuz konsentratsiyasi yuqori bo'lgan eritma.

2-rasm. Integral membrana oqsilining etti turi

Membrana sariq rangda tasvirlangan. 1. Yagona transmembran a-spiral (bitopik membrana oqsili). 2. Politopik transmembran a-spiral oqsil. 3. Politopik transmembran b-varaq oqsili. 4. Membrana tekisligiga parallel bo'lgan amfipatik a-spiralning o'zaro ta'siri (tekislikdagi membrana spiral). 5. Hidrofob halqa bilan o'zaro ta'sir qilish. 6. Kovalent bog'langan membrana lipidining o'zaro ta'siri. 7. Membrananing lipidlari bilan ionli yoki elektrostatik o'zaro ta'sirlar.

Membran oqsillarining funktsiyasi

Membran oqsillari barcha organizmlarda hal qiluvchi rol o'ynaydi, bu erda ular membrana retseptorlari sifatida xizmat qiladi. ion kanallari , GPCR (G protein bilan bog'langan retseptorlari) va har xil turdagi oqsillarni tashish . Membran retseptorlari hujayra membranalarida joylashgan bo'lib, ular hujayraning ichki va tashqi muhitlari o'rtasida signallarni uzata oladilar. Membrana transport oqsili (yoki tashuvchisi) biologik membrana bo'ylab ionlar, kichik molekulalar yoki makromolekulalar harakatida ishtirok etadigan membrana oqsilining bir turi. Membran transport oqsili haqida Xalqaro biokimyo va molekulyar biologiya ittifoqi tomonidan tasdiqlangan Transporter tasnifi ma'lumotlar bazasi (yoki TCDB) deb nomlangan batafsil tasnif mavjud. Ion kanallari membranani tashish oqsillarining eng muhim turlaridan biridir. Ion kanalining funktsiyalari tinch membrana potentsialini o'rnatish, hujayra membranasi bo'ylab ionlar oqimini o'tkazish orqali harakat potentsiallarini va boshqa elektr signallarini shakllantirish, sekretor va epiteliya hujayralari bo'ylab ionlar oqimini nazorat qilish va hujayra hajmini tartibga solishni o'z ichiga oladi. Ba'zi fermentlar, shuningdek, membrana oqsillari, masalan, oksidoreduktaza, transferaza yoki gidrolaza. Hujayra yuzasida joylashgan boshqa hujayralar yoki hujayradan tashqari matritsa (ECM) bilan bog'lanishda ishtirok etadigan hujayra yopishish molekulalari hujayralarga bir-birini aniqlash va o'zaro ta'sir qilish imkonini beradi. Masalan, oqsillar, shu jumladan Ig ( immunoglobulin ) immunitet reaktsiyasida ishtirok etadigan super oila. Quyidagi 3-rasmda tushunish oson bo'lishi uchun membrana oqsili funktsiyalari jamlangan.

3-rasm Membran oqsillarining vazifalari

Asosan barcha fiziologik jarayonlardagi markaziy roli tufayli membrana oqsillari tasdiqlangan dori maqsadlarining taxminan 60% ni tashkil qiladi va shuning uchun ularning eksperimental ravishda aniqlangan uchta o'lchovli tuzilmalari –-ga asoslangan dori dizaynida yordam berishga intilmoqda. So'nggi paytlarda sezilarli va sezilarli yaxshilanishlarga qaramay, funktsional va strukturaviy tadqiqotlar uchun etarli miqdorda funktsional katlanmış membrana oqsillarini ifodalash hali ham qiyin vazifadir. Eriydigan sitoplazmatik oqsillar bilan solishtirganda, membrana oqsillarini ifodalashda turli xil qiyinchiliklar mavjud. 1. Membran oqsillari nafaqat sitozolga chiqariladi, balki maqsadli bo'lishi va membranalardagi oxirgi manziliga ko'chirilishi kerak. Xususan, eukaryotik hujayralarda murakkabroq tanib olish va saralash mexanizmlarini talab qiladigan murakkabroq biologik jarayonga ehtiyoj bor. 2. Prokaryotik va eukaryotik ekspressiya tizimlarining nusxalari soni va sig'imi translokatsiya mexanizmlari tufayli cheklangan va translokatsiya faqat membrana oqsillarining alohida guruhlari uchun selektiv bo'lishi mumkin. 3. Strukturaviy va funktsional tadqiqotlar yoki boshqa maqsadlar uchun u hujayradan membrana oqsilini ekspressiyadan so'ng ajratib olish, so'ngra mitsellar yoki lipozomalar kabi sun'iy va belgilangan hidrofobik muhitlarga o'tkazish kerak. Ushbu protsedurada bu juda muhim, chunki membranalar konformatsion aberrasiyalarga yoki membrana oqsillarining ochilishiga olib kelishi mumkin bo'lgan nisbatan qattiq yuvish vositalari bilan parchalanishi kerak. Shuning uchun 150 ga yaqin noyob tuzilmaga ega membrana oqsillaridan strukturaviy ma'lumotlar olinishi ajablanarli emas va faqat

Protein ma'lumotlari bankidagi 7% yozuvlar eriydigan oqsillardan olingan ma'lumotlardan ancha orqada.

Sintezlangan membrana oqsillarining rentabelligi, yaxlitligi, faolligi va barqarorligini belgilaydigan asosiy omillar, asosan, yuqori darajada qayta ishlanadigan transkripsiya va translatsiya mexanizmlarining mavjudligi, mos katlama muhiti, hujayra membranalarining lipid tarkibi, samarali maqsadli tizimlarning mavjudligi va posttranslyatsiya uchun mos yo'llardir. modifikatsiyalar (PTM). Ekspressiya tizimlarida/uyali fonda membrana oqsillarini ularning kelib chiqishi bilan iloji boricha chambarchas bog'liq holda ifodalash eng oqilona strategiya bo'lishi mumkin. Shu bilan birga, individual ekspressiya tizimlarining samaradorligi va ish yuki butunlay boshqacha bo'lib, membrana oqsillarining preparativ miqdori ko'pincha faqat bakterial, xamirturush yoki hujayrasiz tizimlar bilan olinadi (4-rasm).

4-rasm. Membranali oqsillarni ifodalash tizimlarining texnologik dizayni.

Eng mashhur membrana oqsillarini ifodalash tizimlari uchun protokol ishlab chiqishga umumiy nuqtai. Shaxsiy ifoda tizimlari uchun xarakterli asosiy optimallashtirish parametrlari tasvirlangan va eng muhim qismlari ko'rsatilgan. Ba'zi optimallashtirish parametrlari hisobga olinmaydi: vektor yoki maqsadli dizayn, masalan. termoyadroviy texnologiyalar yoki ifoda kassetalarining modifikatsiyalari. Kulrang chiziqlar alohida ekspressiya tizimlaridan foydalangandan so'ng membrana oqsili tuzilmalarini olish muvaffaqiyatini ko'rsatadi, oq chiziqlar esa faqat rekombinant ekspressiyadan keyin olingan membrana oqsili tuzilmalariga mos keladi. (F. Junge va boshqalar.)

To'g'ri ifodalash tizimini tanlashda tadqiqot loyihasining murakkabligi va vaqtini oshirishi mumkin bo'lgan ko'plab omillarni hisobga olish kerak bo'lsa-da, Creative Biolabs keng qamrovli ma'lumotlarni taqdim etishi mumkin. membrana oqsillarini ishlab chiqarish xizmati maqsadli tajribalaringiz uchun optimallashtirish parametri va tizimlarini tanlashga yordam beradi.

Membran oqsili antikori

Membran oqsillari dori vositalarining klinik maqsadlarining katta qismini tashkil qiladi va farmatsevtika va biotexnologik manfaatlar markazidir. So'nggi paytlarda sezilarli va sezilarli yaxshilanishlarga qaramay, funktsional va strukturaviy tadqiqotlar uchun etarli miqdorda funktsional katlanmış membrana oqsillarini ifodalash hali ham qiyin vazifadir. Biroq, Creative Biolabs mutaxassislari tomonidan ishlab chiqilgan membrana oqsillarini tayyorlash uchun hali ham ko'plab strategiyalar mavjud. Shartlariga binoan membranaga qarshi protein antikorlarini topish va ishlab chiqarish , Creative Biolabs fag ko'rsatish orqali immun antikorlar kutubxonasini qurishdan antigenga xos B limfotsitlar sitometriya texnologiyasi orqali mahalliy antikorlarni topishga qadar turli usullarni taqdim etishga qodir. Agar siz yangi membrana oqsili antikorlarini kashf qilmoqchi bo'lsangiz, batafsil ma'lumot olish uchun biz bilan bog'laning.


II. Protein tuzilishining asosiy elementlari

&alpha-spiral oqsil tuzilishining klassik elementidir. Bitta alfa-spiral 35 tagacha qoldiqni buyurtma qilishi mumkin, eng uzun &beta iplar esa atigi 15 ta qoldiqni o'z ichiga oladi va bitta spiral boshqa har qanday individual tuzilish elementiga qaraganda oqsilning barqarorligi va tuzilishiga ko'proq ta'sir qilishi mumkin. &alpha -helices have had an immense influence on our understanding of protein structure because their regularity makes them the only feature readily amenable to theoretical analysis.

ANJIR. 11. Drawing of a typical &alpha -helix, residues 40-51 of the carp muscle calcium binding protein. The helical hydrogen bonds are shown as dotted lines and the main chain bonds are solid. The arrow represents the right-handed helical path of the backbone. The direction of view is from the solvent, so that the side groups on the front side of the helix are predominantly hydrophilic and those in the back are predominantly hydrophobic.

The &alpha -helix was first described by Pauling in 1951 (Pauling va boshqalar., 1951) as a structure predicted to be stable and favorable on the basis of the accurate geometrical parameters he had recently derived for the peptide unit from small-molecule crystal structures. This provided the solution to the long-standing problem of explaining the strength and elasticity of the &alpha -keratin structure and accounting for the appearance of its X-ray fiber diffraction pattern. Helices had frequently been proposed before as the &alpha structure, but none of them could adequately match the diffraction pattern because they had been limited by the implicit assumption that a regular helix would necessarily have an integral number of amino acid residues per turn. In fact, as Pauling first realized, the &alpha -helix has 3.6 residues per turn, with a hydrogen bond between the CO of residue n and the NH of residue n + 4 (see Fig. 11). The closed loop formed by one of these hydrogen bonds and the intervening stretch of backbone contains 13 atoms (including the hydrogen), as illustrated in Fig. 12. In the usual nomenclature for describing the basic structure of polypeptide helices, the &alpha -helix is known as the 3.613-helix, where 3.6 is the number of residues per turn and 13 is the number of atoms in the hydrogen-bonded loop. The rise per residue along the helix axis is 1.5Å.

ANJIR. 12. Illustration of the 13-atom hydrogen-bonded loop which determines the subscript in the description of the &alpha -helix as a 3.613-helix (the 3.6 refers to the number of residues per turn). The 13 atoms are those in the shortest covalently connected path which joins the ends of a single hydrogen bond (the hydrogen is one of the 13 atoms): . . . O&mdashC&mdashN&mdashC &alpha &mdashC&mdashN&mdashC &alpha &mdashC&mdashN&mdashC &alpha &mdashC&mdashN&mdashH . . .

The &alpha -helix received strong experimental support when Perutz (1951) found the predicted 1.5 Å X-ray reflection from hemoglobin crystals and from tilted fibers of keratins. The final conclusive demonstration of the &alpha -helix in globular protein structure came from the high-resolution X-ray structure of myoglobin (Kendrew va boshqalar., 1960). It was shown that the myoglobin helices matched Pauling's calculated structure quite closely, and also that they were all right-handed (for L-amino acids, the left-handed &alpha -helix has a close approach between the carbonyl oxygen and the &beta -carbon). It is easy to determine that, for instance, Fig. 11 is right-handed: if the curled fingers of the right hand are turned in the direction of their tips (as if tightening a screw) and the whole hand is moved in the direction of the outstretched thumb, then a right-handed helical path is traced out. Handedness is an enormously influential parameter in protein structure most features for which handedness can be defined prefer one sense to the other, and the &alpha -helix is only the first of many examples we will encounter.

ANJIR. 13. Stereo drawing of one contour level in the electron density map at 2Å resolution for the residue 54-68 helix in staphylococcal nuclease. Carbonyl groups point up, in the C-terminal direction of the chain the asterisk denotes a solvent peak bound to a carbonyl oxygen in the last turn. Side chains on the left (including a phenylalanine and a methionine) are in the hydrophobic interior, while those on the right (including an ordered lysine) are exposed to solvent.

Figure 13 shows the electron density map at 2 Å resolution for one of the &alpha -helices in staphylococcal nuclease. Bumps for the carbonyl oxygens are clearly visible they point toward the C-terminal end of the helix, and are tipped very slightly outward away from the helix axis. At the top, in the last turn of the helix, there is a carbonyl tipped still further outward and hydrogen-bonded to a solvent molecule (marked with an asterisk). Side chain atoms or waters frequently bond to free backbone positions in the first or last turn of a helix, and hydrogen bonds with water are even more favorable for carbonyls than for NH groups (see Section II,H).

ANJIR. 14. Schematic drawing of the backbone of an all-helical tertiary structure: domain 2 of thermolysin.

With 3.6 residues per turn, side chains protrude from the &alpha -helix at about every 100° in azimuth. Since the commonest location for a helix is along the outside of the protein, there is a tendency for side chains to change from hydrophobic to hydrophilic with a periodicity of three to four residues (Schiffer and Edmundson, 1967). This trend can sometimes be seen in the sequence, but it is not strong enough for reliable prediction by itself. Different residues have weak but definite preferences either for or against being in &alpha -helix: Ala, Glu, Leu, and Met are good helix formers while Pro, Gly, Tyr, and Ser are very poor (Levitt, 1977). &alpha -Helices were central to all the early attempts to predict secondary structure from amino acid sequence (e.g., Davies, 1964 Guzzo, 1965 Prothero, 1966 Cook, 1967 Ptitsyn, 1969 Kotelchuk and Scheraga, 1969 Pain and Robson, 1970) and they are still the feature that can be predicted with greatest accuracy (e.g., Schulz va boshqalar., 1974b Chou and Fasman, 1974b Lim, 1974a Matthews, 1975 Maxfield and Scheraga, 1976 Nagano, 1977b Wu va boshqalar., 1978). [Helix predictions have now reached better than 70% accuracy, using algorithms such as neural nets (Rost and Sander, 2000) or hidden Markov models (Karplus va boshqalar., 1998).] As much as 80% of a structure can be helical, and only seven proteins are known that have no helix whatsoever. Figure 14 shows the second domain of thermolysin, a structure that is predominantly &alpha -helical.

[There are of course now many more than 7 proteins known to have no helicies, but they are still a very small fraction of the total. Further information about amino-acid roles in helix formation is obtained from tabulating position-specific residue preferences (Richardson and Richardson, 1988). This shows that the ends of helices are very different from the central parts, as described below.]

ANJIR. 15. Stereo drawing of a bent helix (glyceraldehyde-phosphate dehydrogenase residues 146-161) with an internal proline. The proline ring produces steric hindrance to the straight &alpha -helical conformation as well as having no NH group available for a hydrogen bond. A proline is the commonest way of producing a bend within a single helix, as well as occurring very frequently at the corners between helices.

The backbone conformational angles for right-handed &alpha -helix are approximately &phi = -60°, &psi = -60° [, more accurately, -63°, -43°] , which is in a favorable and relatively steep energy minimum for local conformation, even ignoring the hydrogen bonds. &alpha -Helices are certainly the most regular pieces of structure to be found in globular proteins, but even so they show significant imperfections. There can be slight bends in the axis of a helix, of any amount from almost undetectable up to about 20° [30°] (e.g., Anderson va boshqalar., 1978), either with or without a break in the pattern of hydrogen bonding. One of the most obvious ways to produce such a bend is with a proline. Proline fits very well in the first turn of an &alpha -helix [especially in position N1] but anywhere further on it not only is missing the hydrogen bond donor but also provides steric hindrance to the normal conformation. It is rare but certainly not unknown in such a position (see Fig. 15). An &alpha -helix is almost invariably made up of a single, connected stretch of backbone (as opposed, for instance, to the backbone changeovers seen for double-helix in transfer RNAs: Holbrook va boshqalar., 1978). Almost the only known exception to this rule is the interrupted helix from subtilisin that is shown in Fig. 16.

ANJIR. 16. An unusual interrupted helix from subtilisin (residues 62-86), in which the helical hydrogen bonds continue to a final turn that is formed by a separate piece of main chain. Such interrupted helices (broken on one side of the double helix) are apparently a fundamental feature of nucleic acid structure as illustrated by tRNA, but are exceedingly rare in protein structure.

[It has continued to prove true that strand changeovers are quite common in RNA molecules, with maintenance of base stacking and double helix geometry across the change, but interrupted &alpha -helices with continuous H-bonding across the break remain extremely rare one further example is in cytochrome C3 (1WAD 74-82), shown in the kinemage II.A_intHlx.kin.]

Click the button at far-left to launch the Java kinemage viewer into a separate browser window. In that window you can interact with the display. Read the specific information in the KiNG text pane.

The generally regular, repeating conformation in the &alpha -helix places all of the charge dipoles of the peptides pointing in the same direction along the helix axis (positive toward the N-terminal end). It has been shown (Hol va boshqalar., 1978) that the overall effect is indeed a significant net dipole for the helix, in spite of shielding effects. The helix dipole may contribute to the binding of charged species to the protein: for example, negative nucleotide phosphates, which are typically found near the N-termini of helices. [The kinemage shows an SO4 ion in sulfate-binding protein bound at the N-termini of 3 helices without any charged side chains.] -->

ANJIR. 17. A short segment of 310 helix from carbonic anhydrase (residues 159-164). Main chain carbonyl oxygens are shown as open circles.

The only other principal helical species besides the &alpha -helix which occurs to any great extent in globular protein structure is the 310-helix (see Fig. 17), with a three-residue repeat and a hydrogen bond to residue n + 3 instead of n + 4. Its backbone conformational angles are approximately &phi = -60°, &psi = -30°, [-70°, -20°] , within the same energy minimum as the &alpha -helix. However, for a long periodic structure the 310-helix is considerably less favorable than the &alpha -helix in both local conformational energy and hydrogen bond configuration. In the refinement of rubredoxin at 1.2 Å resolution, Watenpaugh va boshqalar. (1979) found that bond angles along the main chain were significantly distorted in all four of the regions that have two successive 310-type hydrogen bonds. Long 310 helices are very rare but short pieces of approximate 310-helix occur fairly frequently. Two consecutive residues in 310 conformation form a good tight turn (see Section II,C), and three consecutive 310 residues forming two interlocked tight turns is also fairly common. But another important location for short bits of 310-helix is at the C-terminal end of an &alpha -helix. It is quite common for the last helical turn to tighten up, with hydrogen bonds back to residue n - 3 or else bifurcated hydrogen bonds to both n - 3 and n - 4 (e.g., Watson, 1969). Némethy va boshqalar. (1967) showed that this arrangement is not necessarily quite like 310-helix they described the &alpha II-helix for this sort of position, which retains the helical parameters of an &alpha -helix but tilts the peptide so that the NH points more inward toward the helix axis and at the same time points more toward the n - 3 than the n - 4 carbonyl. The conformations in real proteins show somewhat of a mixture between the &alpha II tilt and the 310 tightening. Figure 18 shows an example. 310 or &alpha II conformation does not tend to occur nearly as often at the N-termini of &alpha -helices. The reason is that the tighter loop with n + 3-type hydrogen bonds requires the group involved to move closer to the helix axis, either by tilting ( &alpha II) or by tightening the helix(310). This motion is easy for the NH group but not for the CO: neighboring carbonyl oxygens would come too close together. [Less often, the end of a helix can loosen rather than tighten or a turn can widen to provide the right geometry for a metal ligand, using the (n+5) H-bonds of what is called a &pi-helix. An example is myohemerythrin 106-112 (2MHR).]

ANJIR. 18. An example of the &alpha II conformation at the end of the A helix in myoglobin (residues 8-17). The normal &alpha -helical hydrogen bonds are shown dotted, while the tighter &alpha II bond is shown by crosses.

Another frequent feature of the C-termini of helices is a residue (usually glycine) in left-handed &alpha conformation with its NH making a hydrogen bond to the CO of residue n - 5 (see Schellman, 1980) this often follows a residue with the 310 or &alpha II bonding described above. [This arrangement has turned out to be very much the commonest way of ending an &alpha -helix. The starting and ending residues that form the transition point half-in and half-out of a helix are now called the helix N-cap and C-cap respectively (Richardson, 1988). The C-cap is most often a glycine in L- &alpha conformation that turns the backbone in the other direction the peptides NH's on either side of the Gly C &alpha make H-bonds back to exposed CO's in the last helical turn, but in inverted sequence order (as shown in kinemage II.A_hlxCaps.kin for the Gly C-cap of helix 4 in 1LMB &lambda repressor). Helix N-cap residues usually have a short sidechain (Asn, Asp, Ser, or Thr) with an oxygen that can H-bond to the exposed backbone NH of residue N2 or N3 (that is, 2 or 3 past the N-cap) in the first helical turn (shown in kinemage for the N-caps of helices 1 and 2 of 1LMB &lambda repressor). A classic helix N-cap also has a "capbox" reciprocal H-bond from the sidechain of residue N3 (Gln, Glu, Ser, or Thr) to the backbone NH of the N-cap residue, in the peptide just before the start of helical conformation (Harper and Rose, 1993). Both N-caps and C-caps often also have a "hydrophobic staple" interaction between suitable sidechains at N' and N4 or C4 and C' (Muñoz va boshqalar., 1995). Proline is actually preferred in the N1 positions (Richardson, 1988).

Click the button at far-left to launch the Java kinemage viewer into a separate browser window. In that window you can interact with the display. Read the specific information in the KiNG text pane.

Good N-caps stabilize both entire proteins (Serrano and Fersht, 1989 Nicholson va boshqalar., 1991) and isolated helical peptides (Lyu va boshqalar., 1993). Glycine C-caps do not stabilize helical peptides (Doig and Baldwin, 1995), but that has been shown to be due to their location at the C-terminus of the chain (Kapp va boshqalar., 2004). Sequences that form good helix caps have become important tools in secondary-structure prediction (Muñoz and Serrano, 1994) and in protein design (Marshall va boshqalar., 2002).]

A few other helical conformations occur occasionally in globular protein structures. The polyproline helix, of the same sort as one strand out of a collagen structure, has been found in pancreatic trypsin inhibitor (Huber va boshqalar., 1971) and in cytochrome c551 (Almassy and Dickerson, 1978). An extended "&epsilon helix" has been described as occurring in chymotrypsin (Srinivasan va boshqalar., 1976). In view of the usual variability and irregularity seen in local protein conformation it is unclear that either of these last two helix types is reliably distinguishable from simply an isolated extended strand however, the presence of prolines can justify the designation of polyproline helix.

[sidebar: Analyses of Helix-Helix Packing]

***The ways in which &alpha -helices pack against one another were initially described by Crick (1953) as "knobs into holes" side chain packing which could work at either a shallow left-handed crossing angle or a steeper right-handed one. Helix-helix interactions have recently been analyzed in more detail by several different groups, using quite varied approaches and points of view. Chothia va boshqalar. (1977) considered the helix contact angles at which ridges formed by rows either of n,n + 3 or of n,n + 4 side chains can pack against each other. They predict three classes (I, II, and III) of contact at angles of -82°, -60° and +19°, respectively (the angle is handed but does not consider direction of the helices). For 25 cases they find a distribution consistent with these classes, although there is better discrimination between classes II and III than between I and II. Richmond and Richards (1978) determine contact residues by calculating solvent accessible area lost on bringing helix pairs together, and model the interactions using helices of close-packed spheres. They find contact classes that match the packing of Chothia's classes II and III, but for approximately perpendicular helices (class I) they find a favorable contact only if the two central residues are glycine or alanine and pack directly on top of each other. In globins the helix axes are about 2Å closer together for steeply angled contacts than for nearly parallel ones, which have a long contact surface between relatively large residues. Figure 19 shows stereo drawings of class II and class III helix contacts. Efimov (1977, 1979) also considers side chain packing as the determinant for helix contacts, but from a rather different theoretical perspective. He first considers what side chain conformations will allow close packing of neighboring hydrophobic side chains on a single helix, then considers how to close-pack side chains of hydrophobic patches on the buried side of two parallel or antiparallel helices, then finally considers the angles for packing together two layers of helices by matching two of the relatively flat hydrophobic surfaces produced in the second step.

Each of these approaches has its advantages the contact nets drawn by Chothia va boshqalar. are the only version that explicitly shows the actual (rather than idealized) residue contacts, but they have made correlations only with the one variable of contact angle. Efimov has obtained a very interesting regularity that successfully predicts side chain conformation at the right and left edges of hydrophobic strips, but has not considered either the interactions directly in between helix pairs in his first step or the possibility that close (as opposed to distant hydrophobic) contacts could occur at steep angles. Richmond and Richards have the advantage of identifying residue contacts in a way that is not influenced by theoretical preconceptions, and they have considered side chain identity (although not conformation) in detail. Because of the great local variability of side chain size and packing and because relatively few examples have yet been analyzed, it is obviously possible to describe a given contact as fitting quite different idealized models. The current large data set of proteins shows a strong tendency for class III (shallow) interactions to be antiparallel and for parallel helix interactions to be class II. It seems likely that the antiparallel up and down helix bundle structures (see Section III,B) would be composed of paradigm class III interactions, and the doubly wound &alpha / &beta structures (see Section III,C) would contain paradigm class II interactions, but none of the 15 proteins analyzed by the above three methods happen to fall into either of those categories. If multiple examples of paradigm classes II and III contacts can be analyzed and compared, it may then be possible to define a meaningfully distinct class of perpendicular contacts.***

ANJIR. 19. Examples of the two commonest types of helix-helix contact: (a) Class II (from hexokinase) with an inter-helix angle of about -60° (b) Class III (from myohemerythrin) with an inter-helix angle of about +20°.

[Analysis of the general geometry of helix packing is still a fairly open issue, but several aspects of the problem have progressed. An interesting treatment of helix packing in terms of alternate edges of polyhedra (Murzin and Finkelstein, 1988) fits well for many but not all structures. The common and biologically important case of coiled-coils (belonging to the low-angle, class III case) has been very thoroughly and successfully described (O'Shea va boshqalar., 1991), and a rare type of low-angle contact at much closer distances has been described (Gernert va boshqalar., 1995). Perpendicular T-junction contacts have proven important in Ca ++ -binding "E-F hands" (Kretsinger, 1980) and DNA-binding helix-turn-helix motifs (Steitz va boshqalar., 1982).]


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Izohlar:

  1. Maddock

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  6. Oskar

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