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Protein Folding

Protein Folding

Protein Folding

Protein Folding

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.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

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.
The...

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

Amyloid Fibrils

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins. Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils.
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Related Experiment Video

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Microfluidic Mixers for Studying Protein Folding

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Functionally Relevant Specific Packing Can Determine Protein Folding Routes.

Shilpa Yadahalli¹, Shachi Gosavi²

¹National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; Manipal University, Madhav Nagar, Manipal 576104, India; Bioinformatics Institute (A*STAR), Singapore 138671, Singapore.

Journal of Molecular Biology

|January 3, 2016

Summary

Investigating protein folding routes reveals functional insights. Specific aromatic residue packing in the CORE region of E. coli ribonuclease H (ecoRNase-H) dictates its folding pathway, highlighting a link between protein structure and function.

Keywords:

E. coli RNase-H computational protein folding energetic heterogeneity folding mechanism substrate binding

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Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Protein folding mechanisms are influenced by functional residues.
Investigating folding routes may reveal protein functional regions.
Escherichia coli ribonuclease H (ecoRNase-H) folding and function are well-studied.

Purpose of the Study:

To computationally study ecoRNase-H folding using molecular dynamics simulations.
To identify key residues and structural features determining the protein's folding route.
To explore the relationship between folding mechanisms and protein function.

Main Methods:

Utilized molecular dynamics simulations with structure-based models of varying complexity.
Compared models predicting the experimentally determined folding route with simpler models.
Analyzed the role of specific aromatic residue clustering in the CORE region.

Main Results:

A specific packing of six aromatic residues in the CORE region was identified as crucial for early CORE folding and determining the folding route.
This specific packing and the involved residues are conserved across various E. coli-like RNase-Hs.
The identified residues are involved in substrate binding or interaction in both ecoRNase-H and human RNase-H.

Conclusions:

The folding mechanism of ecoRNase-H is shaped by functional requirements, specifically substrate binding.
Understanding specific packing and folding routes offers insights into protein function.
Proposed mutations to engineered HIV RNase-H based on specific packing observations to enhance function.