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Principal Investigator: Bernard R Brooks
Organization: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
Fiscal Year: 2020
Award: $359,079
Funding agency: National Heart Lung and Blood Institute
Traditional molecular modeling is performed at atomic resolution, which relies on X-ray and NMR experiments to provide structural information. When dealing with biomolecular assemblies of millions of atoms, atomic description of molecular objects becomes very computational inefficient. We developed a method that uses map objects for molecular modeling to efficiently derive structural information from experimental maps, as well as conveniently manipulate map objects, perform conformational search directly using map objects. This development work has been implemented into CHARMM as the EMAP module. This implementation enables CHARMM to manipulate map objects, including map input, output, comparison, docking, etc.
Protein-protein docking using map objects
Protein-protein docking is a molecular modeling strategy to predict biomolecular complexes and assemblies. Traditional protein-protein docking is performed at atomic resolution, which relies on X-ray and NMR experiments to provide structural information. When deal with biomolecular assemblies of millions of atoms, atomic description of molecular objects becomes very computational inefficient. This article describes a development work that introduces map objects to molecular modeling studies to efficiently derive complex structures through map-map conformational search. This method has been implemented into CHARMM as the EMAP command and into AMBER in its SANDER program. This development enables molecular modeling and simulation to manipulate map objects, including map input, output, comparison, docking, etc. Through map objects, users can efficiently construct complex structures through protein-protein docking as well as from electron microscopy maps according to low map energies. Using a T-cell receptor variable domain and Acetylcholine Binding Protein (ACHBP) as example systems, we showed the application to model an energetic optimized complex structure according to a complex map. The map objects serves as a bridge between high resolution atomic structures and low resolution image data.
Map restrained Self-guided Langevin dynamics simulation study of SARS-CoV-2 spike ectodomain
The emergence of SARS-CoV-2 has resulted over 3 million infections and more than 200,000 deaths. Coronavirus spike (S) glycoproteins promote entry into cells and are the main target of antibodies. It has been shown that SARS-CoV-2 S uses angiotensin-converting enzyme 2 (ACE2) to enter cells and that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, correlating with the efficient spread of SARS-CoV-2 among humans.
Coronavirus entry into host cells is mediated by the transmembrane spike (S) glycoprotein that forms homotrimers protruding from the viral surface . S comprises two functional subunits responsible for binding to the host cell receptor (S1 subunit) and fusion of the viral and cellular membranes (S2 subunit). Coronavirus entry into susceptible cells is a complex process that requires the concerted action of receptor-binding and proteolytic processing of the S protein to promote virus-cell fusion. As the coronavirus S glycoprotein is surface-exposed and mediates entry into host cells, it is the main target of neutralizing antibodies (Abs) upon infection and the focus of therapeutic and vaccine design.
Conformational transition of SARS-CoV-2 spike is critical for its function to interact with ACE2 and enter host cells. The mechanism of the opening and possibility to mediate this process is the focus of research in development of vaccines. This research benefits from two main aspects, the information extraction from cryo-EM maps and the ability to reproduce the opening process. The map-restrained Self-guided Langevin dynamics method (MapSGLD) developed in this lab is a perfect tool for this type of research. This method accurately extract structure information from cryo-EM maps and achieve large scale conformational search through SGLD to achieve the goal of reproduce conformational evolvement from one state to another. Along the conformational path many opportunities for mediate the process can be discovered and studied. Current, the cryo-EM maps of the open and close state of the SARS-CoV-2 spike ectodomain are available, which provide us unprecedent opportunity to study the mechanism with MapSGLD. It is found that SARS-CoV polyclonal antibodies inhibit SARS-CoV-2 spike-mediated entry into cells. MapSGLD simulation of antibody-spike interaction will provide structure and energetic insight for vaccine development.
Additional SARS-CoV2 simulations
The SARS-Cov2 spike glycoprotein undergoes a structural transition in order to become activated and primed to infect humans. We have developed a workflow using our GPU hardware and OpenMM software that can quickly generate different mutations and protonation states of the spike protein, and simulate them with very high throughput. We are currently studying the role of protonation states in this conformational change to understand if, and how, varying pH can serve as a trigger for the cascade of events that lead to infection.
Ionic Strength Induced Protein-Protein Interactions
Protein kinases are dynamic and can adopt many conformational states, including active, inactive, and intermediate states which can represent an array of structural features that distinguish the ability of the protein to bind other molecules. Revealing the transitions between the conformational states of protein complexes is critical for effective rational design, as it would allow deeper insights into the structure function properties. Improper signaling of the nuclear factor-B (NF-B) pathway plays a critical role in many inflammatory disease states including cancer, stroke, and viral infections. While the signaling pathways are known, how these molecular mechanisms respond to changes in the intracellular microenvironment such as pH, ionic strength, and temperature, remains elusive. Molecular dynamics simulations were used to investigate how mutations and the ionic strength affect dimerization of the protein assembly to probe the affinity for tyrosine and serine phosphorylation activation mechanisms. Intermolecular interactions, thermodynamic properties, and conformational changes were compared among the inactive, active, and null states of the kinase. Results suggest that the multimeric assembly mediates a global stability for the enzyme that influences the activity of IKK and offers insight into which activation mechanism is preferred.
Terms: <2019 novel coronavirus><2019-nCoV><3-D structure><3-dimensional structure><3D structure><ATP-protein phosphotransferase><Acetylcholine><Adopted><Affect><Affinity><Amber><Angiotensin Converting Enzyme><Angiotensin I-Converting Enzyme><Antibodies><Apoplexy><Binding><Binding Proteins><Biological><Brain Vascular Accident><CD143 Antigens><Cancers><Carboxycathepsin><Cell Body><Cell Communication and Signaling><Cell Signaling><Cell fusion><Cells><Cellular Membrane><Cerebral Stroke><Cerebrovascular Apoplexy><Cerebrovascular Stroke><Cessation of life><Chemicals><Classification><CoV S protein><CoV glycoprotein S><CoV spike glycoprotein><CoV spike protein><Communities><Complex><Computational Technique><Computer software><Computing Methodologies><Coronaviridae><Coronavirus><Coronavirus glycoprotein S><Coronavirus spike protein><Cryo-electron Microscopy><Cryoelectron Microscopy><Crystallization><Data><Death><Development><Dimerization><Dipeptidyl Peptidase A><Disease><Disorder><Docking><Electron Cryomicroscopy><Electron Microscopy><Enzyme Stability><Event><FRET><Fluorescence Resonance Energy Transfer><Förster Resonance Energy Transfer><Genetic Alteration><Genetic Change><Genetic defect><Glycoproteins><Goals><Human><Image><Infection><Inflammatory><Information Retrieval><Information extraction><Intracellular Communication and Signaling><Ionic Strengths><Kinase Family Gene><Kinases><Kininase A><Kininase II><L-Serine><Lead><Ligand Binding Protein><Ligand Binding Protein Gene><MHC Receptor><Macromolecular Structure><Major Histocompatibility Complex Receptor><Malignant Neoplasms><Malignant Tumor><Maps><Mediating><Methods><Modeling><Modern Man><Molecular><Molecular Configuration><Molecular Conformation><Molecular Dynamics Simulation><Molecular Interaction><Molecular Modeling Nucleic Acid Biochemistry><Molecular Modeling Protein/Amino Acid Biochemistry><Molecular Models><Molecular Stereochemistry><Molecular Structure><Mutation><NMR Spectrometer><NMR Spectroscopy><Nuclear><Output><Pathway interactions><Pb element><Peptidyl-Dipeptidase A><Phosphorylation><Phosphotransferase Gene><Phosphotransferases><Play><Process><Property><Protein Binding><Protein Dimerization><Protein Kinase><Protein Phosphorylation><Protein Region><Proteins><Proteolytic Clipping><Proteolytic Processing><Receptor Cell><Receptors, Antigen, T-Cell><Research><Research Support><Resolution><Roentgen Rays><Role><SARS Virus><SARS corona virus><SARS coronavirus><SARS-Associated Coronavirus><SARS-CoV><SARS-CoV-2><SARS-CoV2><SARS-Related Coronavirus><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related coronavirus 2><Serine><Severe Acute Respiratory Syndrome Virus><Severe Acute Respiratory Syndrome corona virus><Severe Acute Respiratory Syndrome coronavirus><Severe acute respiratory syndrome coronavirus 2><Signal Pathway><Signal Transduction><Signal Transduction Systems><Signaling><Single Crystal Diffraction><Software><Spectroscopy><Spectrum Analyses><Spectrum Analysis><Stroke><Structure><Study models><Surface><System><Systematics><T-Cell Receptor><Techniques><Temperature><Therapeutic><Thermodynamic><Thermodynamics><Transphosphorylases><Tyrosine><Vaccine Design><Variant><Variation><Viral><Viral Diseases><Virus><Virus Diseases><Work><Wuhan coronavirus><X Ray Crystallographies><X-Radiation><X-Ray Crystallography><X-Ray Diffraction Crystallography><X-Ray Radiation><X-Ray/Neutron Crystallography><X-ray><Xray><Xray Crystallography><biological signal transduction><bound protein><brain attack><cerebral vascular accident><cerebrovascular accident><computational methodology><computational methods><computer based method><computer methods><computing method><conformation><conformational conversion><conformational state><conformational transition><corona virus><coronavirus S protein><coronavirus spike glycoprotein><cryo-EM><cryoEM><design><designing><develop a vaccine><development of a vaccine><developmental><disease-causing mutation><electron tomography><experiment><experimental research><experimental study><genome mutation><glycogen synthase a kinase><heavy metal Pb><heavy metal lead><hydroxyalkyl protein kinase><imaging><inhibiting antibody><insight><intermolecular interaction><macromolecular assembly><macromolecule><malignancy><model-based simulation><models and simulation><molecular assembly><molecular assembly/self assembly><molecular dynamics><molecular modeling><molecular self assembly><molecular size><neoplasm/cancer><neutralizing antibody><nuclear magnetic resonance spectroscopy><pathway><peptide structure><phosphorylase b kinase kinase><polyclonal antibody><programs><protein complex><protein protein interaction><protein structure><protein structures><proteins structure><protonation><receptor binding><receptor bound><severe acute respiratory syndrome-CoV><simulation><social role><structural biology><three dimensional structure><tomography><tool><vaccine development><vaccine formulation><viral infection><virus infection><virus-induced disease>