NDLI: An amino acid code for ß-sheet packing structure.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Joo, Hyun Tsai, Jerry
Description	Author Affiliation: Joo H ( Department of Chemistry, University of the Pacific, Stockton, California, 95212.)
Abstract	To understand the relationship between protein sequence and structure, this work extends the knob-socket model in an investigation of ß-sheet packing. Over a comprehensive set of ß-sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the two types of four-residue packing cliques necessary to describe ß-sheet packing were characterized. Both occur between two adjacent hydrogen bonded ß-strands. First, defining the secondary structure packing within ß-sheets, the combined socket or XY:HG pocket consists of four residues i, i+2 on one strand and j, j+2 on the other. Second, characterizing the tertiary packing between ß-sheets, the knob-socket XY:H+B consists of a three-residue XY:H socket (i, i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, two types of knob-sockets are found: side-chain and main-chain sockets. The amino acid composition of the pockets and knob-sockets reveal the sequence specificity of ß-sheet packing. For ß-sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side-chain and main-chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for ß-sheet structure and provide an intuitive topological mapping of ß-sheet packing.
File Format	HTM / HTML
ISSN	08873585
e-ISSN	10970134
DOI	10.1002/prot.24569
Journal	Proteins: Structure, Function, and Bioinformatics
Issue Number	9
Volume Number	82
Language	English
Publisher	Wiley-Liss
Publisher Date	2014-09-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Protein Structure, Tertiary Research Support, N.i.h., Extramural Amino Acid Sequence Protein Structure, Secondary Discipline Biochemistry Models, Molecular Metabolism Protein Folding Protein Interaction Mapping Protein Interaction Maps Proteins Hydrogen Bonding
Content Type	Text
Resource Type	Article
Subject	Structural Biology Biochemistry Molecular Biology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

Protein models: the Grand Challenge of protein docking.

Comparative structural analysis of the binding domain of follicle stimulating hormone receptor.

Helix kinks are equally prevalent in soluble and membrane proteins.

An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements.

Folding thermodynamics of ß-hairpins studied by replica-exchange molecular dynamics simulations.

Crystal structure of BamB bound to a periplasmic domain fragment of BamA, the central component of the ß-barrel assembly machine.

Buried water molecules in helical transmembrane proteins.

ß-Bulges: extensive structural analyses of ß-sheets irregularities.

An amino acid code for ß-sheet packing structure.

Similar Documents

A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

Protein models: the Grand Challenge of protein docking.

Comparative structural analysis of the binding domain of follicle stimulating hormone receptor.

Helix kinks are equally prevalent in soluble and membrane proteins.

An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements.

Folding thermodynamics of ß-hairpins studied by replica-exchange molecular dynamics simulations.

Crystal structure of BamB bound to a periplasmic domain fragment of BamA, the central component of the ß-barrel assembly machine.

Buried water molecules in helical transmembrane proteins.

ß-Bulges: extensive structural analyses of ß-sheets irregularities.

An amino acid code for ß-sheet packing structure.