scholarly journals Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily

2017 ◽  
Vol 27 (2) ◽  
pp. 421-430 ◽  
Author(s):  
Zheng Dong ◽  
Hongyu Zhou ◽  
Peng Tao
Keyword(s):  
Protein Sequence ◽  
Pas Domain ◽  
Functional Evolution ◽  
Sequence Structure ◽  
Structure And Dynamics ◽  
Evolution Analysis ◽  
Novel Approach

scholarly journals Characterization of the SARS‐CoV‐2 E Protein: Sequence, Structure, Viroporin and Inhibitors

2021 ◽  
Author(s):  
Yipeng Cao ◽  
Rui Yang ◽  
Imshik Lee ◽  
Wenwen Zhang ◽  
Jiana Sun ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Sequence Structure ◽  
E Protein

Nonlinear Signal Analysis Methods in the Elucidation of Protein Sequence−Structure Relationships

2002 ◽  
Vol 102 (5) ◽  
pp. 1471-1492 ◽  
Author(s):  
Alessandro Giuliani ◽  
Romualdo Benigni ◽  
Joseph P. Zbilut ◽  
Charles L. Webber, ◽  
Paolo Sirabella ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Signal Analysis ◽  
Sequence Structure ◽  
Analysis Methods ◽  
Nonlinear Signal ◽  
Nonlinear Signal Analysis

scholarly journals Glycan synthesis, structure, and dynamics: A selection

2013 ◽  
Vol 85 (9) ◽  
pp. 1759-1770 ◽  
Author(s):  
Robert Pendrill ◽  
K. Hanna M. Jonsson ◽  
Göran Widmalm
Keyword(s):  
Structural Information ◽  
3D Structure ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Conformational Space ◽  
Torsion Angles ◽  
Structure And Dynamics ◽  
Novel Approach ◽  
Acetyl Group ◽  
Experimental Spectroscopy

Glycan structural information is a prerequisite for elucidation of carbohydrate function in biological systems. To this end we employ a tripod approach for investigation of carbohydrate 3D structure and dynamics based on organic synthesis; different experimental spectroscopy techniques, NMR being of prime importance; and molecular simulations using, in particular, molecular dynamics (MD) simulations. The synthesis of oligosaccharides in the form of glucosyl fluorides is described, and their use as substrates for the Lam16A E115S glucosyl synthase is exemplified as well as a conformational analysis of a cyclic β-(1→3)-heptaglucan based on molecular simulations. The flexibility of the N-acetyl group of aminosugars is by MD simulations indicated to function as a gatekeeper for transitions of glycosidic torsion angles to other regions of conformational space. A novel approach to visualize glycoprotein (GP) structures is presented in which the protein is shown by, for example, ribbons, but instead of stick or space-filling models for the carbohydrate portion it is visualized by the colored geometrical figures known as CFG representation in a 3D way, which we denote 3D-CFG, thereby effectively highlighting the sugar residues of the glycan part of the GP and the position(s) on the protein.

scholarly journals Variable gap penalty for protein sequence–structure alignment

2006 ◽  
Vol 19 (3) ◽  
pp. 129-133 ◽  
Author(s):  
M.S. Madhusudhan ◽  
Marc A. Marti-Renom ◽  
Roberto Sanchez ◽  
Andrej Sali
Keyword(s):  
Protein Sequence ◽  
Structure Alignment ◽  
Sequence Structure
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