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A Survey of the Structural Parameters Used for Computational Prediction of Protein Folding Process

  • Gulshan Khalique
  • Tambi Richa
Chapter

Abstract

Proteins play cardinal roles in carrying out many biological activities such as immune system reactions, signal transduction, gene expression, storage, translocation and much more. In general, proteins are synthesized in ribosomes of eukaryotic organisms as linear polypeptide chains, which then acquire unique biologically active three-dimensional (3D) structures (also known as their native state) in a few seconds or so. Each protein has a unique structure which dictates its function. Proteins fold into one or more conformations in order to perform its biological functions. Conformations can be defined as the alternative structures of the same protein, and shift between them are called conformational changes. This is propelled by a number of non-covalent interactions like ionic interactions, hydrogen bonding, hydrophobic packing and van der Waals forces. In this chapter, we first discuss the structural hierarchy of proteins. The journey of a protein from its primary structure to its native state is explained here. In the second part, we briefly discuss the ‘protein folding problem’ which will allow the readers to understand the complexities involved in this process – the most essential and fundamental process for life. Both experimental and in silico methods are used to study this process. Here, we focus on the in silico methods – especially the initial step where the 3D structure of proteins is examined and the vital factors are determined. Finally, we introduce our readers to the structural determinants of proteins obtained statistically by analysing the residue- and atom-level contacts formed by its structure.

Keywords

Protein structure Structural hierarchy Protein folding problem Folding rate Structural descriptors Protein Data Bank 

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Gulshan Khalique
    • 1
  • Tambi Richa
    • 2
    • 3
  1. 1.Jain UniversityBangaloreIndia
  2. 2.Tokyo University of Agriculture and TechnologyTokyoJapan
  3. 3.Current Address: Banerjee LabMohammed Bin Rashid UniversityDubaiUAE

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