Molecular dynamics simulation of alpha-lactalbumin and calcium binding c-type lysozyme.
Abstract: Alpha-lactalbumins (LAs) and c-type lysozymes (LYZs) are two classes of proteins which have a 35-40% sequence homology and share a common three dimensional fold but perform different functions. Lysozymes bind and cleave the glycosidic bond linkage in sugars, where as, alpha-lactalbumin does not bind sugar but participates in the synthesis of lactose. Alpha-lactalbumin is a metallo-protein and binds calcium, where as, only a few of the LYZs bind calcium. These proteins consist of two domains, an alpha-helical and a beta-strand domain, separated by a cleft. Calcium is bound at a loop situated at the bottom of the cleft and is important for the structural integrity of the protein. Calcium is an ubiquitous intracellular signal in higher eukaryotes and structural changes induced on calcium binding have been observed in a number of proteins. In the present study, molecular dynamics simulations of equine LYZ and human LA, with and without calcium, were carried out. We detail the differences in the dynamics of equine LYZ and human LA, and discuss it in the light of experimental data already available and relate it to the behavior of the functionally important regions of both the proteins. These simulations bring out the role of calcium in the conformation and dynamics of these metallo-proteins. In the calcium bound LA, the region of the protein around the calcium binding site is not only frozen but the atomic fluctuations are found to increase away from the binding site and peak at the exposed sites of the protein. This channeling of fluctuations away from the metal binding site could serve as a general mechanism by which the effect of metal binding at a site is transduced to other parts of the protein and could play a key role in protein-ligand and/or protein-protein interaction.
Publication Date: 1999-04-09 PubMed ID: 10195284DOI: 10.1093/protein/12.2.129Google Scholar: Lookup
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- Comparative Study
- Journal Article
- Research Support
- U.S. Gov't
- P.H.S.
Summary
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The research focuses on studying the dynamic behavior of two types of proteins – Alpha-lactalbumins and c-type lysozymes – using molecular simulations. The goal is to understand the differences in their reactions with and without calcium present, and how calcium affects their structure, function, and interaction with other proteins and ligands.
Background and Purpose of the Study
- Alpha-lactalbumins (LAs) and c-type lysozymes (LYZs) are two types of proteins that exhibit 35-40% sequence homology and share similar three-dimensional configuration, despite performing different functions.
- Lyzsozymes bind to and break down sugars, whereas alpha-lactalbumins do not bind sugar but are involved in the synthesis of lactose. Additionally, alpha-lactalbumins, as metallo-proteins, bind calcium while only few of the lysozymes bind calcium.
- The researchers believed it was important to understand the dynamics of these proteins, especially regarding the effect of calcium on their structural integrity, function and potential interactions with other proteins or ligands.
Methodology
- The researchers conducted molecular dynamics simulations on equine lysozyme and human alpha-lactalbumin, both in the presence and absence of calcium.
- This provided insights into the differences in their dynamics and how they correspond to experimental data.
Findings
- From the simulations, they noted that the presence of calcium in alpha-lactalbumin makes the region around the calcium binding site “frozen,” with an increase in atomic fluctuations moving away from the binding site, peaking at the protein’s exposed sites.
- This fluctuation channeling away from the metal binding site reveals how the effect of metal binding at a specific location can be transferred to other parts of the protein.
- This discovery could potentially serve as a general mechanism describing how metal-protein interactions affect protein structure and function, including protein-ligand and protein-protein interactions.
Cite This Article
APA
Iyer LK, Qasba PK.
(1999).
Molecular dynamics simulation of alpha-lactalbumin and calcium binding c-type lysozyme.
Protein Eng, 12(2), 129-139.
https://doi.org/10.1093/protein/12.2.129 Publication
Researcher Affiliations
- Laboratory of Experimental and Computational Biology, Division of Biological Sciences, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
MeSH Terms
- Animals
- Calcium / chemistry
- Computer Simulation
- Crystallography
- Horses
- Humans
- Lactalbumin / chemistry
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Muramidase / chemistry
- Protein Conformation
Citations
This article has been cited 3 times.- Woods KN, Pfeffer J. Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes.. Mol Biol Evol 2016 Jan;33(1):40-61.
- Kirberger M, Wang X, Zhao K, Tang S, Chen G, Yang JJ. Integration of Diverse Research Methods to Analyze and Engineer Ca-Binding Proteins: From Prediction to Production.. Curr Bioinform 2010 Mar 1;5(1):68-80.
- Li JH, Liu YQ, Lü P, Lin HF, Bai Y, Wang XC, Chen YL. A signaling pathway linking nitric oxide production to heterotrimeric G protein and hydrogen peroxide regulates extracellular calmodulin induction of stomatal closure in Arabidopsis.. Plant Physiol 2009 May;150(1):114-24.
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