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A Stereochemically-Bent <i>β</i>-hairpin: Scrutiny of Folding by Comparing a Heteropolypeptide and Cognate Oligoalanine

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Open Journal of Physical Chemistry 2014年第3期4卷 81-97页

作者： Kinshuk Raj Srivastava Susheel Durani Department of Chemistry Indian Institute of Technology Bombay Mumbai India Department of Physics and Astronomy Michigan State University East Lansing USA

A poly-L β-hairpin bent stereochemically as a boat-shaped protein of mixed-L,D structure is scrutinized in basis of ordering as minimum of energy specific for its sequenceand solvent. The model suitable for the scrutiny is accomplished by design. A terminally-blocked oligoalanine is nucleated overDPro6-Gly7 and DPro6-LAsp7 dipeptide structures as a twelve-residue β-hairpin and bent stereochemically as a boat-shaped fold. The structure is inverse designed with side chains suitable to bind substrate p-nitophenyl phosphate, a surrogate substrate of acetyl choline and CO2. The designed sequences were proven by spectroscopy and molecular dynamics to order with solvent effects of water and display high binding affinity for the substrate. One of the proteins and a cognate oligoalanine are evolved with molecular dynamics to equilibrium in a solvent bath of water. Molecular dynamics studies establish that heteropolypeptide well ordered as β-hairpin fold and cognate oligoalanine as an ensemble of hairpin-like folds in water. The ordering of cognate oligoalanine as ensembles of hairpin-like folds manifests combined role of water as strong dielectric and weak dipolar solvent of peptides. The roles of stereochemistry and chemical details of sequence in defining polypeptides as energy minima under specific effect of solvent are illuminated and have been discussed.

关键词： Protein Folding Protein Stereochemistry β-hairpin Polyalanine Model Solvent Effects

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Molecular Dynamics Folding Simulation of β-hairpin Protein （1E0Q）

Molecular Dynamics Folding Simulation of β-hairpin Protein ...

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2011 2nd International Conference on Chemical Engineering and Applications（CCEA 2011）

作者： Nur Shima Fadhilah Mazlan Nurul Bahiyah Ahmad Khairudin Faculty of Chemical Engineering Universiti Teknologi Malaysia Malaysia Japan International Institute of Technology Universiti Teknologi Malaysia International Campus Jalan Semarak 54100 Kuala Lumpur Malaysia

The structure and trajectories of the mutant peptide of ubiquitin （PDB ID:1E0Q） has been studied using Molecular Dynamics （MD） *** investigation of protein folding pathway for protein IE0Q had been carried out using MD Simulation for 50 ns at temperature 325 *** this simulation,the protein 1E0Q has folded into its native β-hairpin structure within 5 *** RMSD value as compared to the NMR structure from the first residue to 17 residues is 2.17 ?.It has been observed that Gly 10 had been responsible to promote β-turn which caused the structure to turn into β-*** secondary structure analysis,it is shown that the residue from Thr 6 to Lys 11 has formed a bend in the *** beta strands has also been found comprising residues Glu 2 to Lys 5 and Ile 13 to Glu 16.

关键词： Molecular Dynamics Protein folding β-hairpin

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The Comparison between Random Forest and Support Vector Machine Algorithm for Predicting β-hairpin Motifs in Proteins

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Engineering（科研） 2013年第10期5卷 391-395页

作者： Shaochun Jia Xiuzhen Hu Lixia Sun Department of Physics College of Sciences Inner Mongolia University of Technology Huhhot China

Based on the research of predictingβ-hairpin motifs in proteins, we apply Random Forest and Support Vector Machine algorithm to predictβ-hairpin motifs in ArchDB40 dataset. The motifs with the loop length of 2 to 8 amino acid residues are extracted as research object and thefixed-length pattern of 12 amino acids are selected. When using the same characteristic parameters and the same test method, Random Forest algorithm is more effective than Support Vector Machine. In addition, because of Random Forest algorithm doesn’t produce overfitting phenomenon while the dimension of characteristic parameters is higher, we use Random Forest based on higher dimension characteristic parameters to predictβ-hairpin motifs. The better prediction results are obtained;the overall accuracy and Matthew’s correlation coefficient of 5-fold cross-validation achieve 83.3% and 0.59, respectively.

关键词： Random Forest Algorithm Support Vector Machine Algorithm β-hairpin Motif Increment of Diversity Scoring Function Predicted Secondary Structure Information

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Reliable folding of hybrid tetrapeptides into shortβ-hairpins

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Chinese Chemical Letters 2022年第1期33卷 257-261页

作者： Xue-Yi Sun Yulong Zhong Yao-Hua Li Daniel P.Miller Sagar Buttan Xiang-Xiang Wu Yukun Zhang Quan Tang Hong-Wei Tan Jin Zhu Rui Liu Eva Zurek Zhong-Lin Lu Bing Gong College of Chemistry Beijing Normal UniversityBeijing 100875China Department of Chemistry University at BuffaloThe State University of New YorkBuffaloNY 14260United States Department of Chemistry Hofstra UniversityHempsteadNY 11549United States Academy of Chinese Medical Science Henan University of Chinese MedicineZhengzhou 450046China Chengdu Institute of Organic Chemistry Chinese Academy of SciencesChengdu 610041China

Five hybrid tetrapeptides,each consisting a central dipeptide segment ofα-amino acid residues flanked by two aromaticγ-amino acid residues,are found to fold into well-definedβ-hairpin conformations as shown by NMR,computational study,and X-ray *** turn loop of thisβ-hairpin motif accommodates different two-residueα-amino acid sequences from the highly flexible Gly-Gly,to the more restricted *** presence ofα-amino acid side chains enhances the stabilities of theβ-hairpins with the exception of D-Pro-Gly-which results in *** on this hairpin/turn motif,a variety of different dipeptide sequences ofα-amino acids which rarely occur inβ-turns can be introduced and presented as two-residue loops.

关键词： β-hairpin β-Turn γ-Amino acid NMR X-ray

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