Physics and Evolution of Biological Macromolecules
Principal Investigator

Group Members
Dr. BEREZOVSKY IgorPrincipal Investigator
Dr. GUARNERA EnricoResearch Scientist
Dr. TAN Zhen WahPostdoctoral Fellow
Mr. YIN Chee Peng, MelvinResearch Officer
Mr. TEE Wei Ven PhD student
Ms. AMANGELDINA Aidana PhD student

Research Overview

The group is working on the development of new physical models and bioinformatics computational approaches in the following areas:

  • molecular mechanisms of adaptation to extreme environments with a special interest to protein thermostability;
  • protein functional dynamics and allosteric regulation; and
  • emergence and evolution of the protein function.
More Details

Selected Publications
  1. Tee WV, Guarnera E, Berezovsky IN.
    Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response.
    PLoS Comput Biol. 2018 Jun 18;14(6):e1006228. doi: 10.1371/journal.pcbi.1006228. eCollection 2018 Jun.
    PubMed PMID: 29912863; PubMed Central PMCID: PMC6023240.

  2. Kurochkin IV, Guarnera E, Berezovsky IN.
    Insulin-Degrading Enzyme in the Fight against Alzheimer's Disease.
    Trends Pharmacol Sci. 2018 Jan;39(1):49-58. doi: 10.1016/ Epub 2017 Nov 10.
    PubMed PMID: 29132916.

  3. Guarnera E, Tan ZW, Zheng Z, Berezovsky IN.
    AlloSigMA: allosteric signaling and mutation analysis server.
    Bioinformatics. 2017 Dec 15;33(24):3996-3998. doi: 10.1093/bioinformatics/btx430.
    PubMed PMID: 29106449.

  4. Berezovsky IN, Bastolla U.
    Editorial overview: Proteins: bridging theory and experiment.
    Curr Opin Struct Biol. 2017 Feb;42:viii-x. doi: 10.1016/ Epub 2017 Jan 10. No abstract available.

  5. Kurochkin IV, Guarnera E, Wong JH, Eisenhaber F, Berezovsky IN.
    Toward Allosterically Increased Catalytic Activity of Insulin-Degrading Enzyme against Amyloid Peptides.
    Biochemistry. 2017 Jan 10;56(1):228-239. doi: 10.1021/acs.biochem.6b00783. Epub 2016 Dec 16.

  6. Berezovsky IN, Guarnera E, Zheng Z, Eisenhaber B, Eisenhaber F.
    Protein function machinery: from basic structural units to modulation of activity.
    Curr Opin Struct Biol. 2017 Feb;42:67-74. doi: 10.1016/ Epub 2016 Nov 16. Review.

  7. Berezovsky IN, Guarnera E, Zheng Z.
    Basic units of protein structure, folding, and function.
    Prog Biophys Mol Biol. 2016 Sep 30. pii: S0079-6107(16)30086-4. doi: 10.1016/j.pbiomolbio.2016.09.009. [Epub ahead of print] Review.

  8. Guarnera E, Vanden-Eijnden E.
    Optimized Markov state models for metastable systems.
    J Chem Phys. 2016 Jul 14;145(2):024102. doi: 10.1063/1.4954769. (2016)

  9. Eisenhaber B, Kuchibhatla D, Sherman W, Sirota FL, Berezovsky IN, Wong WC, Eisenhaber F.
    The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.
    Methods Mol Biol. 2016;1415:477-506. doi: 10.1007/978-1-4939-3572-7_25.

  10. Guarnera E, Berezovsky IN.
    Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication.
    PLoS Comput Biol. 2016 Mar 3;12(3):e1004678. doi: 10.1371/journal.pcbi.1004678. eCollection 2016 Mar.

  11. Guarnera E, Berezovsky IN.
    Allosteric sites: remote control in regulation of protein activity.
    Curr Opin Struct Biol. 2016 Apr;37:1-8. doi: 10.1016/ Epub 2015 Nov 10. Review.

  12. Zheng Z, Goncearenco A, Berezovsky IN.
    Nucleotide binding database NBDB--a collection of sequence motifs with specific protein-ligand interactions.
    Nucleic Acids Res. 2016 Jan 4;44(D1):D301-7. doi: 10.1093/nar/gkv1124. Epub 2015 Oct 26.

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