Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation
| Autor: | Shane E. Gordon, John Wagner, Matthew T. Downton, Daniel K. Weber, Matthew A. Perugini |
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| Rok vydání: | 2023 |
| Předmět: |
0301 basic medicine
Protein Conformation Staphylococcus Plasma protein binding Pathology and Laboratory Medicine Biochemistry 01 natural sciences Substrate Specificity Protein structure Enzyme Stability Pyruvic Acid Biochemical Simulations Medicine and Health Sciences Staphylococcus Aureus lcsh:QH301-705.5 Uncategorized Crystallography Ecology biology Physics Ketones Condensed Matter Physics Bacterial Pathogens Chemistry Computational Theory and Mathematics Medical Microbiology Modeling and Simulation Physical Sciences Crystal Structure Pathogens Umbrella sampling Research Article Protein Binding Pyruvate Biophysical Simulations Markov Models Dihydrodipicolinate synthase Stereochemistry Biophysics Molecular Dynamics Simulation 010402 general chemistry Microbiology Catalysis Protein–protein interaction 03 medical and health sciences Cellular and Molecular Neuroscience Genetics Solid State Physics Binding site Protein Interactions Microbial Pathogens Molecular Biology Hydro-Lyases Ecology Evolution Behavior and Systematics Enzyme substrate complex Binding Sites Bacteria Chemical Compounds Organisms Biology and Life Sciences Computational Biology Proteins Active site Probability Theory 0104 chemical sciences Enzyme Activation Kinetics 030104 developmental biology Models Chemical lcsh:Biology (General) biology.protein Acids Mathematics |
| Zdroj: | PLoS Computational Biology, Vol 12, Iss 3, p e1004811 (2016) PLoS Computational Biology |
| DOI: | 10.26181/22028729 |
| Popis: | Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions. Author Summary Interactions between proteins and ligands underpin many important biological processes, such as binding of substrates to their cognate enzymes in the process of catalysis. These interactions are complex, often requiring several intermediate steps to fully transition into the bound state. Here, we have used computational simulation to study binding of pyruvate to Dihydrodipicolinate synthase (DHDPS), an enzyme in the bacterial diaminopimelate pathway. In bacteria, such as the human pathogen S. aureus, DHDPS functions to make building blocks necessary for protein and bacterial cell wall biosyntheses. As the enzyme is absent in humans, yet essential for bacterial growth, DHDPS is a valid target for broad-range antibiotics. However, known DHDPS inhibitors show poor potency. One avenue that has not yet been taken into consideration for inhibitor design is the dynamics of DHDPS’s interaction with its reaction substrates (e.g. pyruvate). Using molecular dynamics simulation, we find that pyruvate binding to DHDPS must pass through a transition intermediate ‘hotspot’ in which the substrate is held in place by a dense network of noncovalent bonds. Given that many of the protein residues involved in this interaction are also shared by DHDPS from many pathogenic bacteria, this binding intermediate ‘hotspot’ may help in development of better broad-range DHDPS inhibitors. |
| Databáze: | OpenAIRE |
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