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Terminus-immobilization effect on peptide conformations and peptide–peptide interactions

Nano Research 2023年第12期16卷 13498-13508页

作者： Wendi Luo Xiaocui Fang Chen Wang Yanlian Yang Bin Tu Qiaojun Fang Laboratory of Theoretical and Computational Nanoscience CAS Key Laboratory for Biological Effects of Nanomaterials&NanosafetyCAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China Sino-Danish Center for Education and Research Beijing 101408China

peptide-modified delivery systems are enabling the improvement of the targeting specificity,biocompatibility,stability,***,the precise design of a peptide-decorated surface for a designated function has remained to be challenging due to a lack of mechanistic understanding of the interactions between surface-bound peptide ligands and their *** by the recent report on pairwise interactions between peptides in the solution state and surface-immobilized state,we used computational simulations to explore the contributing mechanisms underlining the observed binding affinity *** dynamics simulations were performed to sample and compare conformations of homo-octapeptides free in solution(mobile peptides)and bound to the surface(N-terminal fixed peptides).We found that peptides converged to more extended and rigid conformations when immobilized to the surface and confirmed that the extended structures could increase the space available to counter-interacting peptides during the peptide–peptide *** addition,studies on interactions between stationary and mobile peptides revealed that main-chain/side-chain and side-chain/side-chain hydrogen bonds play an important *** presented efforts in this work may provide supportive references for peptide design and modification on the nanoparticle surface as well as guidance for analyzing peptide–receptor interactions through an emphasis on hydrogen bonds during peptide design and an understanding of the influence on the binding affinity by the sequence-dependant conformational changes after peptide immobilization.

关键词： terminus-immobilization peptide conformations peptide–peptide interactions molecular dynamics peptide design

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Zwitterionic peptides:Tunable next-generation stealth nanoparticle modifications

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Bioactive Materials 2023年第9期27卷 113-124页

作者： Clyde Overby Soomin Park Austin Summers Danielle S.W.Benoit Department of Biomedical Engineering University of Rochester RochesterNYUSA Center for Musculoskeletal Research University of RochesterRochesterNYUSA Department of Biology University of Rochester RochesterNYUSA Department of Biology Duquesne UniversityPAUSA Department of Chemical Engineering University of RochesterRochesterNYUSA Materials Science Program University of RochesterRochesterNYUSA Knight Campus for Accelerating Scientific Impact Department of BioengineeringUniversity of OregonEugeneORUSA

Adsorption of proteins to nanoparticles(NPs),a complex process that results in a protein corona,is controlled by NP surface properties that define NP interactions in *** to control adsorbed protein quantity through surface modification have led to improvements in circulation time or ***,current approaches have yet to be identified to control adsorbed protein identities within the ***,we report the development and characterization of diverse zwitterionic peptides(ZIPs)for NP anti-fouling surface functionalization with specific and controllable affinity for protein adsorption profiles defined by ZIP *** serum exposure of ZIP-conjugated NPs and proteomics analysis of the resulting corona,we determined that protein adsorption profiles depend not on the exact composition of the ZIPs but on the sequence and order of charges along the sequence(charge motif).These findings pave the way for developing tunable ZIPs to orchestrate specific ZIP-NP protein adsorption profiles as a function of ZIP charge motif to better control cell and tissue specificity and pharmacokinetics and provide new tools for investigating relationships between protein corona and biological ***,overall ZIP diversity enabled by the diversity of amino acids may ameliorate adaptive immune responses.

关键词： Nanoparticles Protein corona Surface functionalization peptide design Cellular uptake

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finDr:A web server for in silico D-peptide ligand identification

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Synthetic and Systems Biotechnology 2021年第4期6卷 402-413页

作者： Helena Engel Felix Guischard Fabian Krause Janina Nandy Paulina Kaas Nico Hofflin Maja Kohn Normann Kilb Karsten Voigt Steffen Wolf Tahira Aslan Fabian Baezner Salom´e Hahne Carolin Ruckes Joshua Weygant Alisa Zinina Emir Bora Akmeriç Enoch B.Antwi Dennis Dombrovskij Philipp Franke Klara L.Lesch Niklas Vesper Daniel Weis Nicole Gensch Barbara Di Ventura Mehmet Ali Oztürk Signalling Research Centres BIOSS and CIBSS University of FreiburgSchanzlestr.1879104FreiburgGermany Institute of Biology III Faculty of BiologyUniversity of FreiburgSchanzlestr.179104FreiburgGermany Institute of Biology II Faculty of BiologyUniversity of FreiburgSchanzlestr.179104FreiburgGermany AG Roth-Lab for MicroarrayCopying ZBSA-Centre for Biological Systems AnalysisUniversity of FreiburgHabsburgerstrasse 4979104FreiburgGermany Biomolecular Dynamics Institute of PhysicsUniversity of FreiburgHermann-Herder-Strasse 3a79104FreiburgGermany Core Facility Signalling Factory Centre for Biological Signaling Studies(BIOSS)University of FreiburgSchanzlestr.1879104FreiburgGermany Spemann Graduate School of Biology and Medicine(SGBM) University of FreiburgAlbertstraße 19A79104FreiburgGermany Internal Medicine IV Department of MedicineMedical CenterUniversity of FreiburgHugstetter Straße 5579106FreiburgGermany Institute for Biochemistry University of FreiburgAlbertstr.2179104FreiburgGermany

In the rapidly expanding field of peptide therapeutics,the short in vivo half-life of peptides represents a considerable limitation for drug action.D-peptides,consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids(AAs),do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation,resulting in a favourable pharmacokinetic *** experimentally identify D-peptide binders to interesting therapeutic targets,so-called mirror-image phage display is typically performed,whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage *** technique is extremely powerful,but it requires the synthesis of the target in D-form,which is challenging for large *** we present finDr,a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure(https://***/).finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank(PDB)for their ability to bind to the *** a separate,heuristic approach to search the chemical space of 12-mer peptides,finDr executes a customizable evolutionary algorithm(EA)for the de novo identification or optimization of D-peptide *** a proof of principle,we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3(PSMα3),a toxin of methicillin-resistant Staphylococcus aureus(MRSA).We validate the predictions using in vitro binding assays,supporting the success of this *** to conventional methods,finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size *** believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.

关键词： D-peptide Web server Evolutionary algorithm peptide design Molecular docking Mirror-image phage display

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Which peptide could break CDK2/Cyclin E1 interaction?

Which peptide could break CDK2/Cyclin E1 interaction?

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：刘士勇 Haotian Li Hao Chen Chen Zeng Department of Physics Huazhong University of Science and Technology Department of Physics George Washington University

Background:Previous results indicated that the CDK2/Cyclin E1 protein complex, which plays a key role in regulating the cell cycle,could be disrupted by two short peptides TAALS and *** alanine mutagenesis on CDK2 suggests that Y180 and K178 are two possible residues that the peptides target in the CDK2-Cyclin E1 *** design even more potent peptide inhibitors,the detailed binding mechanism needs to be understood clearly. Methods:For the flexible T-loop(amino acids 150-165) on CDK2,an ensemble of ten different conformations was generated by Rosetta for both the inactive CDK2(PDB 1E1X) and the active CDK.2(PDB 1FIN),*** docking by AutoDock onto the ensemble of CDK2 conformations thus mimics a flexible *** resulting CDK2- peptide complex decoys were ranked by three different strategies according to frequency analysis,AutoDock binding energy,or a knowledge-based potential ***,MD simulations on both inactive and active CDK.2,as well as 16 CDK2-peptide decoys were carried out. Results:MD simulations showed that TAALS could dock onto CDK2 between its T-loop and two key residues Y180 and *** stabled a particular T-loop conformation that prevented cyclin from binding to *** TAALS and LAALS bind to the CDK2 similarly based on docking and MD *** findings agree with previous experimental data that TAALS and LAALS are potent *** interestingly,a failed peptide inhibitor RAALF,also known from the previous experiments,was found to move away from the above key pocket sites in our *** observation offered a means to select better ***,based on the methodology described above,six peptides are designed to interrupt CDK2/Cyclin El interface and four of them are found to dissociate the CDK2/Cyclin El complex experimentally by our ***,two such designed peptides(DAALT and YAALQ) inhibit the kinase activity of Cyclin E/Cdk2. Conclusions:A combined computat

关键词： CDK2 peptide design protein-protein interaction AutoDock

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