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Related Concept Videos

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force. 
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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Alternate conformations found in protein structures implies biological functions: A case study using cyclophilin A.

Chandrasekaran Palaniappan1,2, Santhosh Rajendran1,2, Kanagaraj Sekar1

  • 1Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.

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Understanding protein dynamics is key to biomolecular functions. This study reveals that amino acids like Arg, Cys, Met, and Ser frequently adopt alternate conformations, impacting protein function and catalysis.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein dynamics are crucial for functions like ligand binding and catalysis.
  • Key residues often adopt alternate conformations (conformational substates) that are rarely observed in static structures.
  • Investigating these sparsely sampled states offers mechanistic insights into biological processes.

Purpose of the Study:

  • To analyze the occurrence and characteristics of alternate amino acid conformations in protein structures.
  • To investigate the impact of specific mutations on protein dynamics and function using a case study.

Main Methods:

  • Analysis of over 70,000 protein structures to identify alternate conformations.
  • High-resolution X-ray crystallography data analysis.
  • Molecular dynamics simulations (ns-μs timescale) on human cyclophilin A (CypA).

Main Results:

  • Alternate conformations ('A' and 'B') are common for specific amino acids (Arg, Cys, Met, Ser) and found in helical/β-regions.
  • High-resolution X-ray structures frequently exhibit these alternate conformations.
  • A Ser99Thr mutation in CypA impaired alternate conformations of Phe113, affecting the catalytic micro-environment, consistent with experimental data.

Conclusions:

  • Alternate amino acid conformations are significant structural features influencing protein dynamics and function.
  • Understanding these dynamics is vital for deciphering the structure-function-dynamics interplay.
  • The study provides a framework for analyzing protein dynamics and mutation effects at an atomic level.