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Related Concept Videos

Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...

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Updated: Jun 22, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Published on: July 16, 2017

BlockMaster: partitioning protein kinase structures using normal-mode analysis.

Marina Shudler1, Masha Y Niv

  • 1The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot 76100, Israel.

The Journal of Physical Chemistry. A
|June 3, 2009
PubMed
Summary
This summary is machine-generated.

BlockMaster partitions protein structures into rigid and flexible regions. This method reveals novel structural blocks in protein kinases, including a "loop" block that differentiates active and inactive states, aiding drug discovery.

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Last Updated: Jun 22, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein
11:23

Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein

Published on: June 30, 2019

Area of Science:

  • Biochemistry and structural biology
  • Enzymology
  • Drug discovery

Background:

  • Protein kinases are crucial signaling enzymes implicated in numerous diseases, making them key targets for drug development.
  • Regulation of protein kinase activity involves intricate control over their three-dimensional catalytic domain conformations.
  • Understanding these conformational dynamics is essential for designing effective kinase inhibitors.

Purpose of the Study:

  • To develop and validate a computational method, BlockMaster, for dissecting protein structures into semirigid and flexible segments.
  • To apply BlockMaster to protein kinase structures to identify conserved and conformation-specific structural elements.
  • To investigate the differential flexibility of specificity-determining regions in tyrosine versus serine/threonine kinases.

Main Methods:

  • Utilized normal mode analysis to calculate residue-residue correlations for structural partitioning.
  • Developed the BlockMaster algorithm to identify semirigid blocks and flexible regions within protein structures.
  • Applied BlockMaster to diverse protein kinase structures, including active and inactive conformations.

Main Results:

  • BlockMaster accurately partitioned known protein domains and subdomains, validating its efficacy.
  • Identified distinct semirigid blocks within the N-terminal and C-terminal lobes of kinase domains, often with high helical content.
  • Discovered two novel blocks spanning both lobes: a conserved "pivot" block and a conformation-dependent "loop" block that distinguishes active from inactive kinase states.

Conclusions:

  • BlockMaster provides a robust method for analyzing protein structural dynamics and identifying functionally relevant modules.
  • The identified "loop" block offers new insights into the stabilization of inactive kinase conformations, potentially revealing novel therapeutic strategies.
  • The differential flexibility observed in specificity-determining regions may inform the design of selective kinase inhibitors.