Several diverse projects are being pursued. These are the major ones pursued during the past year. Coarse-grained and all-atom molecular dynamics of an ion channel Hyperpolarization-activated cyclic nucleotide-gated 2 (HCN2) ion channels are expressed in the sinoatrial node, dorsal root ganglia and the basal ganglia. They play fundamental roles in electric signaling in nerve, muscle and synapse, but their function and gating mechanism are not completely understood. The overall goal of the project is to gain insight into the mechanism of the HCN2 channel activation upon binding of cyclic adenosine monophosphate (cAMP) to its intracellular C-terminal. Many mechanisms have been proposed for the opening motion propagation in the channel, but they do not completely explain the entire channel behavior. A novel theory states that upon cAMP binding, a part of the HCN2 C-terminal, called the C-helix, stabilizes its secondary structure and moves towards the binding pocket to make contacts with cAMP. Its movement is correlated with the opening conformational change of the channel pore. This theory is being tested using a novel computational method, the self-guided Langevin dynamics (SGLD), which employs guided forces to enhance the low-frequency motion and accelerate the protein conformational search. Starting from the holo state structure and using the distances from tmFRET measurements as constrains, the protein is guided into its apo state. The simulations enable sampling of conformations along this transition, giving insight into the occurring structural changes and ultimately into the HCN2 gating mechanism. Coarse-grained simulations of HCN2 bring information about the folding pathway and additional insight into the stability of the protein with and without ligand. Computational study of the β-galactosidase This work is a collaboration with a cryo-EM laboratory within the NIH. It was sparked by their publishing of a solution structure at 3.2 resolution of β-galactosidase, one of the most used enzymes in molecular biology. Its long sequence (1024 aminoacids) and the fact that it forms a tetramer in order to function, make it an ideal system to apply SGLD and Coarse-grained modeling. This study will add robustness to the cryo-EM technique by comparing the structure and dynamics of the solution cryo-EM structure and the previously published X-ray crystallography structures. 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. Atomic mechanism of the kinesin walking on microtubule Kinesin is a protein belonging to the class of Cytoskeletal motor proteins. Kinesin converts the energy of ATP hydrolysis into stepping movement along microtubules, which supports several vital cellular functions including mitosis, meiosis, and the transport of cellular cargo. Because kinesin is a fundamental protein, further research on the topic will provide important information as to how it functions. Combined with low resolution electron microscopic images, self-guided Langevin dynamics simulations are performed to study molecular motion and conformational change of kinesin motor domain in water and binding with microtubule. SGLD enable simulation to reach the time scale required for conformational change to understand the role of ATP binding and interaction with microtubules. Analysis of the glomerular phosphoproteome Diseases of the kidney filtration barrier are a leading cause of endstage renal failure. Most disorders affect the podocytes, polarized cells that are connected by a unique cell junctional complex, the slit diaphragm. Podocytes require tightly controlled signaling to maintain their integrity, viability and function. Here we provide an atlas of in vivo phosphorylated, glomerulus-expressed proteins including podocyte-specific gene products identified in an unbiased tandem mass spectrometry-based approach. We discovered 2,449 phosphorylated proteins corresponding to 4,171 identified high-confident phosphorylated residues and performed a systematic bioinformatics analysis of this dataset. Among the 146 phosphorylation sites found on proteins abundantly expressed in podocytes, several sites resided close to residues known to be mutated in human genetic forms of proteinuria. One such site discovered on the slit diaphragm protein Podocin, threonine-234 (T234), resides at the interface of Podocin dimers with a distance between both T234 residues of less than 10 Angstrom. We show that phosphorylation critically regulates dimer formation and that this may represent a general principle for the assembly of the large family of PHB-domain containing proteins.
Showing the most recent 10 out of 40 publications
