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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

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Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

Protein Organization

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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Correlation between protein secondary structure, backbone bond angles, and side-chain orientations.

Martin Lundgren¹, Antti J Niemi

¹Department of Physics and Astronomy, Uppsala University, PO Box 803, S-75108 Uppsala, Sweden. martin.lundgren@physics.uu.se

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|September 26, 2012

Summary

Researchers analyzed protein backbone geometry using new visualization techniques. They found correlations between tetrahedral symmetry deviations and secondary structures, proposing an energy function for precise side-chain modeling.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural biology
Computational chemistry
Biophysics

Background:

The tetrahedral geometry around a protein's central carbon (Cα) is fundamental to its structure.
Understanding subtle deviations from ideal geometry is crucial for predicting protein function and dynamics.

Purpose of the Study:

To investigate the fine structure of sp3 hybridized covalent bond geometry in protein backbones.
To develop novel visualization methods for analyzing high-resolution X-ray crystallography data.
To correlate geometric deviations with local protein secondary structures and model side-chain conformations.

Main Methods:

Development of new visualization techniques for Protein Data Bank (PDB) X-ray structures.
Analysis of tetrahedral symmetry around the Cα carbon.
Proposal of a coarse-grained energy function based on Cβ carbon orientations.
Modeling and comparison with experimental data for HP35 chicken villin headpiece.

Main Results:

Observed a correlation between deformations in ideal tetrahedral symmetry and local protein secondary structure.
Developed a universal coarse-grained energy function capable of modeling side-chain geometry with subatomic precision.
Successfully modeled the Cα-Cβ structure of HP35 chicken villin headpiece with a root-mean-square distance deviation under 0.4 Å from experimental data.

Conclusions:

The study reveals a link between protein backbone geometry and secondary structure.
The proposed energy function offers a precise method for predicting side-chain conformations.
These findings advance our understanding of protein structure-function relationships and computational modeling capabilities.