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Protein Folding01:22

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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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Protein Organization01:24

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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 Organization01:13

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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The spatial architecture of protein function and adaptation.

Richard N McLaughlin1, Frank J Poelwijk, Arjun Raman

  • 1Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA.

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|October 9, 2012
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Protein sectors, networks of coevolving amino acids, are crucial for structure and function. Mutations within these sectors drive protein adaptation and specificity changes, offering insights into protein engineering.

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Area of Science:

  • Protein evolution
  • Structural biology
  • Biochemistry

Background:

  • Natural proteins exhibit sparse networks of coevolving amino acids, known as sectors, which are fundamental to their three-dimensional structure and function.
  • Proteins must also possess evolutionary properties like mutation tolerance and adaptability to changing selective pressures.

Purpose of the Study:

  • To investigate the relationship between protein sector architecture and evolutionary properties such as mutation tolerance and adaptive potential.
  • To comprehensively study the impact of single amino acid mutations on protein function and evolution.

Main Methods:

  • Development of a high-throughput quantitative method for comprehensive single-mutation analysis.
  • Systematic substitution of every amino acid position with all other possible amino acids.
  • Utilized a PDZ domain (PSD95(pdz3)) as a model system for experimental validation.

Main Results:

  • Sector positions were found to be functionally sensitive to mutations, while non-sector positions demonstrated greater tolerance.
  • Protein adaptation to altered binding specificities was observed to initiate exclusively through variations within sector residues.
  • A minimal set of two sector mutations was sufficient to quantitatively alter the binding specificity of the PDZ domain.

Conclusions:

  • The sector architecture plays a critical role in both maintaining protein function and enabling adaptive evolution.
  • Functional constraints and adaptive variation are localized within protein sectors, highlighting their importance.
  • These findings have significant implications for understanding protein design principles and for engineering novel protein functions.