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Related Concept Videos

Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

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 Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

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 and Protein Structure02:15

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 can...
Protein Folding01:22

Protein Folding

Overview

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Sequence periodicity and secondary structure propensity in model proteins.

Giovanni Bellesia1, Andrew Iain Jewett, Joan-Emma Shea

  • 1Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA.

Protein Science : a Publication of the Protein Society
|November 26, 2009
PubMed
Summary

Protein folding is primarily driven by the overall amino acid sequence pattern (nonlocal effects), not individual amino acid tendencies (local effects). This finding holds true for small, globular proteins, emphasizing the importance of sequence patterning in protein structure determination.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Folding Dynamics

Background:

  • The relative importance of local (amino acid intrinsic secondary structure propensity) versus nonlocal (amino acid sequence pattern) effects in determining globular protein fold remains a key question.
  • Previous studies using circular dichroism suggested nonlocal patterns dominate secondary structure in peptides.

Purpose of the Study:

  • To quantitatively assess the roles of local and nonlocal factors in governing both secondary and tertiary structures of small, globular proteins.
  • To investigate the influence of amino acid sequence patterns versus intrinsic secondary structure propensities on protein folding.

Main Methods:

  • Development of a coarse-grained computational model for protein folding.
  • Modeling amino acid intrinsic secondary structure propensity using a dihedral potential term, parametrized to experimental data.
  • Quantifying hydrophobic residue attraction based on experimental transfer free energies.

Main Results:

  • Simulations demonstrate that the pattern of polar and nonpolar amino acids (nonlocal effect) dictates protein fold.
  • The protein fold is determined by the sequence pattern even when secondary structure propensities oppose it.
  • The model highlights that tertiary interactions are more influential than secondary structure propensity in protein structure determination.

Conclusions:

  • The overall pattern of amino acids in a sequence is the dominant factor in determining the fold of small, globular proteins.
  • This study supports the fundamental importance of binary patterning in protein folding, even in simplified models.
  • Nonlocal sequence effects override local intrinsic secondary structure propensities in governing protein structure.