Traditional molecular modeling 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. 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. Particularly, we implemented the core-weighted correlation functions to effectively recognize correct fit of component maps in complex maps, and the grid-threading Monte Carlo search algorithm to efficiently construct complex structures from electron density maps. Using EMAP, we are conducting a series collaboration studies. Below is a list of active projects during the past year. 1 Conformational states of KIT extracellular domain in complex with stem cell factor Collaborated with Prof. Savvas Savvides and Dr. Jonathan Elegheert at Ghent University, we studied Conformational states of KIT extracellular domain in complex with stem cell factor based on cryo-EM and SAX images. Constrained molecular dynamic simulations are applied to identify conformation states and ensembles. 2. Tubline formation Collabratoed with Prof. Ruxandra Dima at University of Cincinnati, the formation of a nanotube by tubline dimer was studied. Contacts between intra dimer and inter dimmers are identified, which are important for the geometry of the nanotube. Mutation effect on nanotube properties are studied. 3. Conformational study of Thermosom Collaborated with Prof. George Stan at University of Cincinnati, the conformational states of Thermosome is studied with the map constrained simulation method. The open state conformation was obtained through self-guided molecular dynamics simulation combined with the map constrained simulation method. The simulation results provide insight to the functional pathway of theromsome. It also demonstrate the powerful capability of the map constrained simulation method in bridging the experimental map information to structural and dynamic studies. 4. Molecular modeling and simulation of the gp140/sugar system Colaborated with Dr. Sriram Subramaniam at NCI we performed molecular modeling and simulation study of gp140/sugar system. GP140 is homology modeled mainly based PDB structure, 3jwd. The v1v2 loop region was modeled based on a remote homologeous PDB structure 1ciy. V3 loop was modeled based on PDB structure, 2b4c. Glycan molecules are docked on the gp140 surface using the EMAP module1 of CHARMM2. The gp140-sugar system was fit into the EM map determined from their lab with the EMAP module1 of CHARMM2 to produce the trimer system. The N- and C- terminal motifs of the trimer are fixed by assuming they binding to gp41. The rest part of the trimer is simulated using the self-guided langevin dynamics (SGLD) simulation method to promote conformational changes. In a 1000 ps SGLD simulation, we observed the conformation changed from initial closed state to a open state that is similar to the structure, 3DNO. 5. Calcium ATPase Conformational Transition through Self-Guided Langevin Dynamics Simulation The sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA1a) transport calcium ions from cytoplasm into the reticulum and relaxes the muscle cells. Many crystal structures of SERCA1 in various binding states have been determined, which provide insights into the mechanism of transport Ca2+ across the membrane. Molecular modeling and simulation studies are also devoted to the understanding of this important process. SERCA1a is an integral membrane protein. It comprises a single polypeptide chain of 994 amino acid residues. It is clear from the crystal structures that SERCA has a 10 helices trans-membrane domain (M), an actuator domain (A), a nucleotide binding domain (N), and a phosphorylation domain (P). The Ca2+ transport cycle starts with Ca2E1 through the Ca2+ dependent phosphorylation by ATP, leading to the formation of the Ca2E1P high-energy intermediate. Ca2E1P transits to Ca2E2P, which releases Ca2+ into the lumen of SR and leads to the E2P state. After dephosphorylation, E2P transits to E2 state and closes the luminal gate. Through thermo agitation, E2 transits to E1 by releasing protons into the cytoplasm. E1 has high Ca2+ affinity and binds with Ca2+ to form Ca2E1. To understand the transport mechanism, it is desirable to study the dynamic process during the conformation transition. Self-guided Langevin dynamics (SGLD) is a simulation method capable of studying events with large conformational change. SGLD simulations of SERCA at different binding states produce conformational transitions between conformational states. New conformations for E1.2Ca2+ and E2.P state have been identified and at E2 state the crystal structure is a preferred conformation.
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