Azịza ngwa ngwa
A docking hit is a ranked hypothesis, ọ bụghị nsonaazụ. The question that decides whether a campaign was worth running is narrower than "did the model score well":…
Kedu ihe usoro mmekọrịta nke peptide-protein ga-ekpebi tupu ụgbọ mmiri ọ bụla agbaala
Onye na-ebu ihe ịtụ ahịa Peptide Geo Peptides Usoro nchịkwa nke usoro ọrụ bụ na ọkwa nwere ike ịga n'ihu naanị ihe ọzọ nwere ike ịgha ụgha. Ihe ọ bụla ọzọ dị n'isiokwu a bụ na a na-etinye iwu ahụ ugboro anọ.
Nlele aka aka nwere ike ikpughe ihe akaebe na-efu tupu nnwale, mana akụkọ a anaghị atụ nkesa nke ọdịda mkpọsa. Nyochaa ihe omume usoro, ntọala ọchụchọ, wepụta echiche, njirimara ihe na njikwa nyocha ọnụ.
Ajụjụ ngwá ọrụ na-abịa nke abụọ, na ọ bụ ajụjụ gbasara ihe ọmụma mbụ karịa izi ezi. A na-enyocha docking Peptide na mbụ na CAPRI na agba 28 na 29, na ntule nke sochiri na-arụ ụka na njirisi ndị dị ugbu a chọrọ iwu nhọrọ ka mma, karịsịa ebe a na-amaghị ebe njikọ ahụ (CAPRI peptide gburugburu). Nke ahụ bụ ọnọdụ n'eziokwu nke ubi: a na-atụnyere usoro, a na-asọrịta mpi, ma ọ dịghị akwụkwọ na-akwado usoro ndabara maka ihe ejiri mee ihe. Yabụ na mkpebi ị na-eme tupu ịbanye n'ọdụ ụgbọ mmiri bụ nke njirisi ewepu aka gị chọrọ.
Ntugharị igodo: Otu ogbo nwere ike ịga n'ihu naanị ihe ọkwa ọzọ nwere ike ịgha ụgha.
Nzọụkwụ 1: Kọwaa ọbá akwụkwọ ahụ site n'ịtụle ụdị dị iche iche, ọ bụghị site na ngụkọ
Ntinye: ajụjụ ndu, kwuru dị ka ntụnyere ị chọrọ ime. Omume: idozi ogologo, mkpụrụ akwụkwọ fọdụrụnụ, nkwụsị na njikwa. Mpụta: ndekọ imewe nke otu njikọ njikọ nwere ike wulite na-ajụghị gị ihe ọ bụla. Emechara mgbe ihe ndekọ imewe na-ekwu ihe mere ọbá akwụkwọ a ji zaa ajụjụ a na ihe ọ na-amachaghị ekpuchi.
Mkpuchi na-agwụ ike adịghị, na usoro-oghere mgbakọ na mwepụ na-edozi esemokwu ngwa ngwa. Oghere 7-mer na-ejide usoro 1.28 × 10⁹, 10-mer 1.024×10¹³, na 15-mer 3.2768×10¹⁹, megide ụlọ ngosi ihe ngosi-ụlọ ọba akwụkwọ gbara gburugburu ndị otu 10⁹ (usoro-oghere mgbakọ na mwepụ). Ulo ụlọ ahụ bụ mgbakọ n'usoro n'usoro, ọ bụghị oke tụrụ, ma nkwubi okwu na-ejide uru ọ bụla bara uru: ihe fọrọ nke nta ka ọ bụrụ isii ma ọ bụ asaa fọdụrụ ka ị na-enyocha, na-agụghị ọnụ.
Nke a bụ ebe iche iche-sampling peptidomics na-enweta ọnọdụ ya. Ị na-ahọrọ otu panel nke na-ekpuchi kemịkalụ na ụdị dị iche iche nke peptides isi iyi karịa otu peptide kwa njiri mara., ma ị na-ekwu otú ahụ na ndekọ imewe. Ụkpụrụ ime ụlọ ọba akwụkwọ nke ekwuputara n'akwụkwọ ọrụ nke anyị na-etinye ọnọdụ ọdịda n'ụzọ doro anya: Ọbá akwụkwọ peptide nwere ike daa ogologo oge tupu njikọ Geopeptides Onye na-eweta Peptide cyclic amalite ma ọ bụrụ na imewe adabaghị ajụjụ ndu. Ogologo, ndakota, mkpụrụ akwụkwọ fọdụrụnụ na mmụgharị niile nwere ọnụọgụ peptide niile, mgbagwoju mgbagwoju anya na nyocha nke nyocha, nke mere na imepụta ọba akwụkwọ peptide ekwesịghị ịkwụsị na nhọrọ usoro. Njikwa dị n'otu ndekọ: ihe eji eke ama ama, a scrambled version, na peptide ị na-atụ anya na ọ ga-ada.
Nzọụkwụ 2: Gbaa nyocha nyocha wee nyefee tebụl peptide nwere pronance
Ntinye: raw LC-MS/MS faịlụ na ndekọ-ejizi ihe ndekọ. Omume: chọọ n'enweghị nkọwapụta enzyme, nwere mgbanwe mgbanwe gbasawanye na njikwa FDR nke ezubere iche. Mpụta: okpokoro peptide na-ebu pronance nke ya. Emechara mgbe otu docking nwere ike iyo, re-ọkwa ma chebe ndepụta ahụ na-emegheghị otu faịlụ raw. Ụlọ ọrụ Peptide cyclic
Tọọ ma nyochaa njikwa nchọpụta ụgha maka usoro ọrụ peptidomics n'ezie. Ngwakọta ihe ọmụmụ nke peptide na nzacha protein enweghị ike ikwe nkwa na-erughị 1% peptide FDR na dataset ọzọ, karịsịa na nchọta na-enweghị nkọwapụta enzyme ma ọ bụ jiri mgbanwe gbasaa. Peptides nke parabolic
Ndebiri mkpesa adịlarị. Ndepụta mkpesa MIAIPE, emepụtara n'okpuru HUPO maka immunopeptidomics, chọrọ ikwupụta ma njirimara dabere na usoro ma ọ bụ de novo, ngwá ọrụ ndepụta kacha elu na paramita ya, ntọala search engine, na nzacha ọ bụla etinyere ya (Ndekọ mkpesa MIAIPE). Biri ihe owuwu ya ọbụlagodi maka ihe nlele na-abụghị nke ọrịa. Otu ubi ọzọ dị mfe ichefu: usoro nyocha nke mkpokọta peptidomics na-aga site na nlele tupu ọgwụgwọ site na mmịpụta, ntakiri, Nyocha MS na njirimara, na mmịpụta ga-adị ngwa ngwa iji zere mmebi nke enzymatic na-aga n'ihu. Peptides dị na nlele ahụ bụ nha nwere akụkọ njikwa, ya mere dekọọ ya.
Nzọụkwụ 3: Jiri ọdụ ụgbọ mmiri bute ụzọ, ma gụọ akara ahụ dị ka ọkwa karịa mmekọrịta
Ntinye: okpokoro peptide. Omume: họrọ protocol site na ogologo peptide, steeti nnabata na ma ị nwere ozi saịtị mbụ. Mpụta: Tebụlụ pose dị n'usoro nke e dekọrọ na protocol na criterion. Emechara mgbe Ahịrị ọ bụla na-ekwu nke protocol mepụtara ya na nke etinyere n'ụkpụrụ ịga nke ọma.
Ọnụego ịga nke ọma e bipụtara ekwenyeghị, na esemokwu ahụ bụ ihe ọmụma. HADDOCK's peptide protocol, na-amalite site na mgbakọ atọ-conformation, ruru 79.4% ụdị anabatara maka bound receptor megide peptide na-enweghị njikọ na 69.4% maka unbound/unbound (HADDOCK's peptide protocol). Akụkọ benchmark nke HPEPDOCK 33.3% top-10 ịga nke ọma na 57 ikpe enweghị oke, na-ebili ka 72.6% mgbe ewepụtara saịtị njikọ (Ihe nrịbama ụkpụrụ HPEPDOCK). Ihe nrịbama nke ụzọ docking peptide na-etinye CABS-dock na 53.0% agbụ na 37.0% ewepu na peptiDB, na AutoDock CrankPep na 85.7% na LEADS-PEP n'okpuru mbelata RMSD siri ike na ọnọdụ mpaghara (ihe nrịbama nke ụzọ docking peptide). Nsonaazụ peptide AlphaFold2 na-agba ọsọ 75% n'ime 1.5 Å mgbe a mara motif njide na 36% n'ime 2.5 Å mgbe ọ bụghị (Nsonaazụ peptide nke AlphaFold2).
Ọnụọgụ ndị ahụ abụghị tebụl otu. Ha dị iche na dataset, ogologo peptide na ihe ịga nke ọma criterion, na mgbasa na-egosipụta njirisi dị ka ụzọ. Gịnị na-enyefe bụ ntụziaka nke mmetụta. Ndochi ụgbọ mmiri kpuru ìsì bụ ajụjụ siri ike karịa ọdụ ụgbọ mmiri na-eduzi saịtị, ọ bụ ya mere HADDOCK ji bụrụ ọdụ ụgbọ mmiri na-ebute ozi: na-egbochi mmekọrịta dị mgbagwoju anya site na mutagenesis, MS, NMR ma ọ bụ nchekwa na-echekwa ihe ị maralarị (HADDOCK bụ ọdụ ụgbọ mmiri na-ebute ozi). CABS-dock na-agba ọsọ kpuru ìsì, na-ewere peptide dị ka nke zuru oke na-agbanwe ma na-alọghachi trajectories na ụyọkọ kama ịbụ otu ọkwa (CABS-dock na-agba ọsọ kpuru ìsì). Ntụle AlphaFold 3 n'onwe ya na-akọpụta protein na mgbochi mmadụ wee kwuo na ọ na-ebu amụma ihe owuwu kwụ ọtọ., ọ bụghị ensembles (Ntụle nke AlphaFold 3). Họrọ protocol dabara na amata mbụ ị nwere, wee gụọ mmepụta dị ka ọkwa.
Nzọụkwụ 4: Kpebisie ike na klaasị dị mma, wee kpebie ihe kwesịrị njikọ
DockQ na-enyocha mgbagwoju anya buru amụma megide usoro ntụnye aka ma bara uru maka nlegharị anya nlegharị anya. Ọ nweghị ike weta eriri dị mma maka ụlọ akwụkwọ akụkọ amaghị akwụkwọ ntụaka ya. Maka nhọrọ a na-atụ anya ya, jiri ihe akaebe ntụkwasị obi emeziri, iche iche, enwere ike yana atụmatụ nnabata nnwale akọwapụtara nke ọma. Usoro DockQ.
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Nkọwapụta bụ ebe mgbakọ na mwepụ na ndị otu nnwale na-atụkarị onwe ha. Kpọọ ụdị usoro aha ya, mgbanwe na saịtị ya, na ụdị counterion, n'ihi na mgbanwe nke ọ bụla n'ime ha na-agbanwe ihe ị na-anwale. Rịọ maka asambodo nyocha nwere ịdị ọcha nyocha-HPLC, njirimara mass-spectrometry na ọdịnaya peptide net, ma gbakwunye ule endotoxin ma ọ bụ nyocha counter-ion ebe nyocha chọrọ ya. Onye na-ebubata ihe dị ka MOL mgbanwe nwere ike ibuga ngwugwu ahụ n'akụkụ peptide, nke bụ ihe kpatara ya iji dozie data achọrọ n'ihu usoro karịa ka emechara ya.
Nzọụkwụ 5: Kwenye na nnwale, dakọtara nyocha na ajụjụ a jụrụ
Ntinye: peptides synthesized na data nza ha. Omume: mee nyocha nke ọgụgụ ya zara ajụjụ a kapịrị ọnụ. Mpụta: nsonaazụ njide ma ọ bụ enweghị njikọ yana ọnọdụ nha ya. Emechara mgbe Enwere ike iji nsonaazụ ya tụnyere amụma docking na usoro abụọ na-anabata.
Dakọtara nyocha ahụ na nkwupụta ahụ. Ntụnye n'ọdụ ụgbọ mmiri na-ebu amụma saịtị njikọ yana geometry dị nso; nyocha asọmpi ma ọ bụ usoro mutagenesis na-anwale saịtị ahụ, ebe a na-ekekọta nha kpọmkwem na-anwale mmekọrịta. Ha anaghị agbanwe agbanwe, na nsonaazụ efu sitere na nyocha na-ezighi ezi agwaghị gị ihe ọ bụla gbasara pose ahụ. Ebe nchekwa data mmekọrịta SKEMPI na-egosi ihe kpatara usoro a ga-eji jiri nọmba mee njem: Ndenye ya na-edekọ usoro nha na ọnọdụ okpomọkụ, na elu plasmon resonance na fluorescence spectroscopy na-achịkwa akwụkwọ (nchekwa data mmekọrịta SKEMPI). “Kd ọ bụla” ị na-atụnyere megide na-eketa echiche nke ụzọ abụọ ahụ, yabụ kọwapụta ọnọdụ nke gị ma tụnye ya ka ọ dị ka.
Ihe nkwekọ ekwenyesiri ike na-akwado nkwupụta njide, mana ọ naghị egosi na amụma ahụ e buru n'amụma ma ọ bụ kwado usoro ụgbọ mmiri dum. Nsonaazụ adịghị ejikọta na adịghị ike na-enye ihe ọmụma mgbe nyocha nyocha, A na-aghọta àgwà ihe onwunwe na ọnọdụ.
Ihe ọdịda nkịtị na otu esi ejide ha na aka
Ụkpụrụ dị n'azụ tebụl bụ na ọdịda ọ bụla dị ọnụ ala iji jide elu na ọnụ ala ala. Tebụl peptide na-enweghị ntọala FDR ya enweghị ike ịmegharị ọzọ, yabụ ndị otu ụgbọ mmiri na-atụkwasị obi ma ọ bụ wughachi ya. Enweghị ike ịtụgharị ndepụta aha ọkwa na-enweghị protocol ya, ya mere ezi pose na a kechioma pose anya yiri. Nkọwapụta na-efunahụ mpempe akwụkwọ na-emepụta peptide nke nwere ike na-akpa àgwà dị iche na nke egosipụtara.
Mmechi
Iwu ahụ na-agwakwa gị otu esi eme mkpọsa ma ọ bụ kpee onye mmekọ na-enye otu. Jụọ onye ọkwa nke na-emepụta ihe artifact, ma ahọpụtara protocol docking ka ọ dabara na amata nke mbụ dị, na ma arịrịọ njikọ ahụ na-eburu njirisi nnabata nke ya. Onye mmekọ nke nwere ike ịza ajụjụ atọ ahụ nwere usoro ọrụ. Onye mmekọ nke na-edu akara nwere ọkwa.
Ebe akwụkwọ na-agwụ, kpebisie ike na nka. Ọ bụrụ na tebụl peptide bịarutere na-enweghị paramita ọchụchọ, jụọ ha tupu ị banye n'ọdụ ụgbọ mmiri. Ọ bụrụ na tebụl pose abata na-enweghị akara ya, jụọ nke etinyere. Ọ bụrụ na nkọwapụta bịarutere na-enweghị ụdị usoro, jụọ nke molecule a na-ajụ ka ị nwalee. Ajụjụ ndị ahụ efughị ihe ọ bụla ma dozie ọtụtụ arụmụka ahụ.
Mgbanwe MOL na-akwado usoro ọrụ a n'ebe a na-emepụta ihe ndị ahụ: Pentide ọba akwụkwọ imewe na ogologo ogologo, nkwụsị, mutation na njikwa mgbagha, na njikọ omenala na akwụkwọ nyocha nke na-ekpuchi ịdị ọcha HPLC, njirimara MS na ọdịnaya peptide. Ọ bụrụ na ị na-eme mkpọsa, ziga anyị ebumnuche gị, ogologo peptide na atụmatụ nyocha, ma anyị ga-enyocha ike ya na gị.
Nkpughe nke onye mbipụta: MOL Mgbanwe na-enye ọrụ peptide ma nwee mmasị azụmahịa na isiokwu a. Ogo ọrụ na nkwupụta ikike bụ nkwupụta ndị na-ebubata ya; nnweta na ịrụ ọrụ maka otu ihe owuwu chọrọ ihe akaebe akọwapụtara nke ọma.
