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Related Concept Videos

Protein and Protein Structure02:15

Protein and Protein Structure

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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.
A protein's shape is critical to its function. For example, an enzyme...
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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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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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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Simulating protein evolution in sequence and structure space.

Yu Xia1, Michael Levitt

  • 1Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.

Current Opinion in Structural Biology
|April 20, 2004
PubMed
Summary
This summary is machine-generated.

Simulating protein evolution reveals how natural proteins evolved. Evolutionary dynamics and selection pressures shape protein sequences, structures, and functions.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Proteins are a selected subset of all possible sequences and structures.
  • Evolutionary simulations offer insights into protein evolution dynamics.

Purpose of the Study:

  • To understand evolutionary dynamics of protein populations.
  • To investigate how selection pressures shape protein sequences and structures.
  • To identify dominant selection pressures on natural proteins.

Main Methods:

  • Simulations using simplified and all-atom protein models.
  • Mapping native structure, stability, and folding rate in sequence space.
  • Utilizing lattice proteins and computational protein design.

Main Results:

  • Lattice protein studies revealed organizational principles of the sequence/structure map.
  • Evolutionary simulations highlighted the role of fitness landscapes and population dynamics.
  • All-atom simulations identified key selection pressures on protein sequences and structures.

Conclusions:

  • Protein evolution is shaped by complex interactions between sequence, structure, and function.
  • Computational models are crucial for deciphering evolutionary pathways and selection pressures.
  • Understanding these principles aids in predicting and designing novel protein functionalities.