ArticleJournal of biomolecular structure & dynamics2014
Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.
Article in Journal of biomolecular structure & dynamics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed, 123 citations in OpenAlex.
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- Synchronized motion of interface residues for evaluating protein-RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates.Protein science : a publication of the Protein Society · 2024Article
- Mechanical Properties of a Solvated Biomolecule: RGD (1FUV) Peptide.International journal of molecular sciences · 2024Article
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- Unveiling Switching Function of Amino Acids in Proteins Using a Machine Learning Approach.Journal of chemical theory and computation · 2023Article
- Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study.International journal of molecular sciences · 2023Article
- Exploiting conformational dynamics to modulate the function of designed proteins.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structural insights into the effect of mutations in the spike protein of SARS-CoV-2 on the binding with human furin protein.Heliyon · 2023Article
- Engineering the Active Site Lid Dynamics to Improve the Catalytic Efficiency of Yeast Cytosine Deaminase.International journal of molecular sciences · 2023Article
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- Beyond structure: Deciphering site-specific dynamics in proteins from double histidine-based EPR measurements.Protein science : a publication of the Protein Society · 2022Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure-function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca(2+) removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca(2+) removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein-ligand binding, including the concept of the free energy landscape (FEL) of the protein-solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.
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