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Protein and Protein Structure

Protein and Protein Structure

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.
A protein's shape is critical to its function. For example, an enzyme...

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.
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Protein Folding

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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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Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

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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Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Structural dynamics of pentapeptide repeat proteins.

Shenyuan Xu¹, Michael A Kennedy¹

¹Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.

|June 18, 2020

Summary

This summary is machine-generated.

Pentapeptide repeat proteins (PRPs) exhibit unique β-helix structures. Molecular dynamics and normal mode analysis reveal correlated and anticorrelated motions crucial for their function and stability.

Keywords:

amide exchange rates beta turn hydrogen-deuterium exchange molecular dynamics simulation normal mode analysis pentapeptide repeat protein protein dynamics protein stability

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Biophysics
Structural Biology
Bioinformatics

Background:

Pentapeptide repeat proteins (PRPs) form a large superfamily found across diverse species, notably in cyanobacteria.
PRPs feature characteristic pentapeptide repeats that fold into right-handed quadrilateral β-helices, termed repeat-five-residue (Rfr)-folds.
PRPs are classified into groups 1 and 2 (antibiotic resistance) and group 3 (unknown functions).

Purpose of the Study:

To investigate the biophysical characteristics of PRPs, focusing on Rfr-fold thermal stability, hydrogen bond dynamics, and backbone motion.
To analyze the structural dynamics of group 1, 2, and 3 PRPs using computational methods.

Main Methods:

Conducted 20 nanosecond molecular dynamics (MD) simulations.
Performed all-atom normal mode analysis (aaNMA) on selected PRPs.
Analyzed MD cross-correlation matrices and aaNMA data.

Main Results:

Identified strong correlated motions between adjacent coils and weak coupled motions between distant coils in PRPs.
Detected slow anticorrelated motions between adjacent coils via aaNMA.
Hypothesized these motions are essential for accessing exchange-competent states for amide hydrogen solvent exchange.

Conclusions:

PRP structural dynamics involve coordinated movements between coils, facilitating functional states.
Anticorrelated motions are key for solvent exchange in β-ladder and β-turn hydrogen bonds.
Understanding these dynamics provides insights into PRP function and stability.