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Amino Acid Function and Docking Site Prediction Through Combining Disease Variants, Structure Alignments, Sequence Alignments, and Molecular Dynamics: A Study of the HMG Domain
BMC Bioinformatics
  • Jeremy W. Prokop, University of Akron Main Campus
  • Thomas C. Leeper, University of Akron Main Campus
  • Zhong-Hui Duan
  • Amy Milsted, University of Akron Main Campus
Document Type
Article
Publication Date
3-13-2012
Disciplines
Abstract
Background: The DNA binding domain of HMG proteins is known to be important in many diseases, with the Sox sub-family of HMG proteins of particular significance. Numerous natural variants in HMG proteins are associated with disease phenotypes. Integrating these natural variants, molecular dynamic simulations of DNA interaction and sequence and structure alignments give detailed molecular knowledge of potential amino acid function such as DNA or protein interaction. Results: A total of 33 amino acids in HMG proteins are known to have natural variants in diseases. Eight of these amino acids are normally conserved in human HMG proteins and 27 are conserved in the human Sox sub-family. Among the six non-Sox conserved amino acids, amino acids 16 and 45 are likely targets for interaction with other proteins. Docking studies between the androgen receptor and Sry/Sox9 reveals a stable amino acid specific interaction involving several Sox conserved residues. Conclusion: The HMG box has structural conservation between the first two of the three helixes in the domain as well as some DNA contact points. Individual sub-groups of the HMG family have specificity in the location of the third helix, DNA specific contact points (such as amino acids 4 and 29), and conserved amino acids interacting with other proteins such as androgen receptor. Studies such as this help to distinguish individual members of a much larger family of proteins and can be applied to any protein family of interest.
Required Publisher's Statement

© 2012 Prokop et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Comments

© 2012 Prokop et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citation Information
Jeremy W. Prokop, Thomas C. Leeper, Zhong-Hui Duan and Amy Milsted. "Amino Acid Function and Docking Site Prediction Through Combining Disease Variants, Structure Alignments, Sequence Alignments, and Molecular Dynamics: A Study of the HMG Domain" BMC Bioinformatics Vol. 13 (2012)
Available at: http://works.bepress.com/thomas_leeper/4/