scholarly journals A systematic analysis of the beta hairpin motif in the Protein Data Bank

2021 ◽  
Author(s):  
Cory D. DuPai ◽  
Bryan W. Davies ◽  
Claus O. Wilke
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Systematic Analysis ◽  
Beta Hairpin

scholarly journals A systematic analysis of the beta hairpin motif in the Protein Data Bank

2020 ◽  
Author(s):  
Cory D. DuPai ◽  
Bryan W. Davies ◽  
Claus O. Wilke
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Design Principles ◽  
Structural Motif ◽  
Systematic Analysis ◽  
Designed Proteins ◽  
Key Characteristics ◽  
Hairpin Structures ◽  
Beta Hairpin ◽  
Proteins And Peptides

AbstractThe beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here we systematically probe all 49,000 unique beta hairpin substructures contained within the Protein Data Bank (PDB) to uncover key characteristics correlated with stable beta hairpin structure, including amino acid biases and enriched inter-strand contacts. We also establish a set of broad design principles that can be applied to the generation of libraries encoding proteins or peptides containing beta hairpin structures.ImportanceThe beta hairpin motif is a common protein structural motif that is known for its stability and varied activity in diverse proteins. Here we use nearly fifty thousand beta hairpin substructures from the Protein Data Bank to systematically analyze and identify key characteristics of the beta hairpin motif. Ultimately, we provide a set of design principles for the generation of synthetic libraries encoding proteins containing beta hairpin structures.

scholarly journals A systematic analysis of protein–carbohydrate interactions in the Protein Data Bank

Glycobiology ◽  
2020 ◽  
Author(s):  
Yiwei Cao ◽  
Sang-Jun Park ◽  
Wonpil Im
Keyword(s):  
Binding Site ◽  
Protein Data Bank ◽  
Structural Similarity ◽  
Data Bank ◽  
Biological Processes ◽  
Feature Points ◽  
Systematic Analysis ◽  
Pattern Similarity ◽  
Atomic Interactions ◽  
Backbone Structure

Abstract Protein–carbohydrate interactions underlie essential biological processes. Elucidating the mechanism of protein–carbohydrate recognition is a prerequisite for modeling and optimizing protein–carbohydrate interactions, which will help in discovery of carbohydrate-derived therapeutics. In this work, we present a survey of a curated database consisting of 6,402 protein–carbohydrate complexes in the Protein Data Bank (PDB). We performed an all-against-all comparison of a subset of nonredundant binding sites, and the result indicates that the interaction pattern similarity is not completely relevant to the binding site structural similarity. Investigation of both binding site and ligand promiscuities reveals that the geometry of chemical feature points is more important than local backbone structure in determining protein–carbohydrate interactions. A further analysis on the frequency and geometry of atomic interactions shows that carbohydrate functional groups are not equally involved in binding interactions. Finally, we discuss the usefulness of protein–carbohydrate complexes in the PDB with acknowledgement that the carbohydrates in many structures are incomplete.

scholarly journals The Protein Data Bank: data distribution and query functionality

2002 ◽  
Vol 58 (s1) ◽  
pp. c214-c214
Author(s):  
W. F. Bluhm ◽  
T. Battistuz ◽  
E. Clingman ◽  
N. Deshpande ◽  
W. Fleri ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Data Distribution ◽  
Data Bank

FLIPPER: predicting and characterizing linear interacting peptides in the Protein Data Bank

2021 ◽  
pp. 166900
Author(s):  
Alexander Miguel Monzon ◽  
Paolo Bonato ◽  
Marco Necci ◽  
Silvio C.E. Tosatto ◽  
Damiano Piovesan
Keyword(s):  
Protein Data Bank ◽  
Data Bank

scholarly journals Validation and correction of Zn–Cys x His y complexes

2016 ◽  
Vol 72 (10) ◽  
pp. 1110-1118 ◽  
Author(s):  
Wouter G. Touw ◽  
Bart van Beusekom ◽  
Jochem M. G. Evers ◽  
Gert Vriend ◽  
Robbie P. Joosten
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Model Validation ◽  
Data Bank ◽  
Zinc Complexes ◽  
Zinc Ions ◽  
Tetrahedral Complex ◽  
Context Sensitive

Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn–Cys distances and Cys–Zn–Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.

scholarly journals Protein Data Bank: the single global archive for 3D macromolecular structure data

2018 ◽  
Vol 47 (D1) ◽  
pp. D520-D528 ◽  
Author(s):  
◽  
Stephen K Burley ◽  
Helen M Berman ◽  
Charmi Bhikadiya ◽  
Chunxiao Bi ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Structure Data ◽  
Data Bank ◽  
Macromolecular Structure

scholarly journals New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

2017 ◽  
Vol 27 (1) ◽  
pp. 95-102 ◽  
Author(s):  
Akira R. Kinjo ◽  
Gert-Jan Bekker ◽  
Hiroshi Wako ◽  
Shigeru Endo ◽  
Yuko Tsuchiya ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Data Bank
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