Characterization of protein secondary structure

2004 ◽  
Vol 23 (3) ◽  
pp. 78-87 ◽  
Author(s):  
M.K. Ganapathiraju ◽  
J. Klein-Seetharaman ◽  
N. Balakrishnan ◽  
R. Reddy
Keyword(s):  
Secondary Structure ◽  
Protein Secondary Structure

A detailed shape characterization of regular polypeptide conformations

1995 ◽  
Vol 73 (2) ◽  
pp. 241-248 ◽  
Author(s):  
Gustavo A. Arteca
Keyword(s):  
Secondary Structure ◽  
Protein Secondary Structure ◽  
Molecular Size ◽  
Molecular Geometry ◽  
Molecular Shape ◽  
Local Analysis ◽  
Structural Motifs ◽  
Protein Backbones ◽  
Shape Characterization

Regular polypeptide conformations include secondary structural motifs such as α-helices and β-strands. The occurrence of some regular conformation is usually deduced from a local analysis of dihedral angles. However, the value of a dihedral angle in itself does not provide any information on the conformation's "shape." This drawback can be circumvented with global, rather than local, macromolecular shape descriptors. Recently, fractal exponents have been proposed as a source of such descriptors. Yet, this approach does not fully capture all essential shape features, since protein backbones are not fractal. In this work, we deal instead with a more "natural" characterization of the polymer's global shape that uses both the chain's geometry and "topology." For the geometry, we study the behaviour of molecular size and anisometry. For the chain's folding features, we study the self-entanglements in a polymer fold. We compute these descriptors for all relevant secondary structural motifs. By using self-entaglements and molecular geometry, we provide a view of secondary structure that is both conceptually appealing and also more discriminating than previous ones in the literature. Keywords: molecular shape analysis, protein secondary structure, self-entanglements.

Identification of novel β-mannan- and β-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules

2001 ◽  
Vol 356 (3) ◽  
pp. 791-798 ◽  
Author(s):  
Anwar SUNNA ◽  
Moreland D. GIBBS ◽  
Peter L. BERGQUIST
Keyword(s):  
Secondary Structure ◽  
Protein Secondary Structure ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Experimental Characterization ◽  
Carbohydrate Polymers ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Long Chain

Many glycoside hydrolases, which degrade long-chain carbohydrate polymers, possess distinct catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). On the basis of conserved protein secondary structure, we describe here the identification and experimental characterization of novel type of mannanase-associated mannan-binding module and also characterization of two CBM family 4 laminarinase-associated β-glucan-binding modules. These modules are predicted to belong to a superfamily of CBMs which include families 4, 16, 17, 22 and a proposed new family, family 27.

Characterization of Tamm-Horsfall Urinary Glycoprotein

1973 ◽  
Vol 31 ◽  
pp. 420-421
Author(s):  
John P. Robinson ◽  
J. David Puett
Keyword(s):  
Electron Microscopy ◽  
Circular Dichroism ◽  
Secondary Structure ◽  
Quaternary Structure ◽  
Normal Adult ◽  
Morphological Properties ◽  
Adult Males ◽  
Circular Dichroïsm ◽  
Urinary Glycoprotein

Much work has been reported on the chemical, physical and morphological properties of urinary Tamm-Horsfall glycoprotein (THG). Although it was once reported that cystic fibrotic (CF) individuals had a defective THG, more recent data indicate that THG and CF-THG are similar if not identical.No studies on the conformational aspects have been reported on this glycoprotein using circular dichroism (CD). We examined the secondary structure of THG and derivatives under various conditions and have correlated these results with quaternary structure using electron microscopy.THG was prepared from normal adult males and CF-THG from a 16-year old CF female by the method of Tamm and Horsfall. CF female by the method of Tamm and Horsfall.

A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
Author(s):  
Elaheh Kashani-Amin ◽  
Ozra Tabatabaei-Malazy ◽  
Amirhossein Sakhteman ◽  
Bagher Larijani ◽  
Azadeh Ebrahim-Habibi
Keyword(s):  
Systematic Review ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Web Of Science ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Protein Secondary Structure ◽  
Structural Features ◽  
Prediction Tools ◽  
Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

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