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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
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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....

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Related Experiment Video

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Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

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Conformational Studies of Polyprolines.

Haizhen Zhong¹, Heather A Carlson¹

¹Department of Medicinal Chemistry, College of Pharmacy, The University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065.

Journal of Chemical Theory and Computation

|December 3, 2015

Summary

This summary is machine-generated.

Polyproline peptides favor trans-proline type II (PII) conformations. This study reveals two novel polyproline structures (PIII and PIV) and clarifies how peptide rotamers and torsions dictate helix handedness.

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Area of Science:

Biochemistry
Computational Chemistry
Structural Biology

Background:

Proline-rich sequences are key recognition elements in peptides.
Polyproline type II (PII) is the predominant conformation for trans-proline oligomers.
Understanding polyproline conformations is crucial for protein structure and function.

Purpose of the Study:

To investigate the conformational preferences of polyproline sequences using computational methods.
To identify and characterize novel secondary structures of polyprolines.
To elucidate the factors influencing polyproline helix handedness.

Main Methods:

Gas-phase quantum mechanics calculations (B3LYP/6-31G*) were employed.
Solvent effects were estimated to model condensed-phase behavior.
A survey of proline oligomers in the Protein Data Bank was conducted.

Main Results:

Calculations confirmed the energetic favorability of all-trans-polyproline conformations over all-cis-polyprolines (PI).
Two new polyproline structures, polyproline type III (PIII) and type IV (PIV), were proposed.
PIII exhibits characteristics of both PI and PII, potentially acting as a conformational intermediate.
Handedness of polyproline helices is influenced by both cis/trans rotamers and ψ torsion angles.

Conclusions:

The study validates existing polyproline conformation models and introduces novel structures.
PIII and PIV represent significant additions to the known secondary structures of polyprolines.
The findings provide a deeper understanding of polyproline conformational flexibility and its determinants.