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Computational Research in Molecular Chemistry
Lipoprotein-associated phospholipase A2: A paradigm for allosteric regulation by membranesMouchlis, V.D., D. Hayashi, A.M. Vasquez, J. Cao, J.A. McCammon, E.A. DennisTo Proc. Natl. Acad. Sci. USA January 11, 119 (2) e2102953118 (2022)    
Lipoprotein-associated phospholipase A2 (Lp-PLA2) associates with low- and high-density lipoproteins in human plasma and specifically hydrolyzes circulating oxidized phospholipids involved in oxidative stress. The association of this enzyme with the lipoprotein’s phospholipid monolayer to access its substrate is the most crucial first step in its catalytic cycle. The current study demonstrates unequivocally that a significant movement of a major helical peptide region occurs upon membrane binding, resulting in a large conformational change upon Lp-PLA2 binding to a phospholipid surface. This allosteric regulation of an enzyme’s activity by a large membrane-like interface inducing a conformational change in the catalytic site defines a unique dimension of allosterism. The mechanism by which this enzyme associates with phospholipid interfaces to select and extract a single phospholipid substrate molecule and carry out catalysis is key to understanding its physiological functioning. A lipidomics platform was employed to determine the precise substrate specificity of human recombinant Lp-PLA2 and mutants. This study uniquely elucidates the association mechanism of this enzyme with membranes and its resulting conformational change as well as the extraction and binding of specific oxidized and short acyl-chain phospholipid substrates. Deuterium exchange mass spectrometry coupled with molecular dynamics simulations was used to define the precise specificity of the subsite for the oxidized fatty acid at the sn-2 position of the phospholipid backbone. Despite the existence of several crystal structures of this enzyme cocrystallized with inhibitors, little was understood about Lp-PLA2‘s specificity toward oxidized phospholipids.
Investigating intrinsically disordered proteins with Brownian dynamicsAhn, S.H., G.A. Huber, J.A. McCammonFrontiers in Molecular Biosciences in press (2022)    
Intrinsically disordered proteins (IDPs) have recently become systems of great interest due to their involvement in modulating many biological processes and their aggregation being implicated in many diseases. Since IDPs do not have a stable, folded structure, however, they cannot be easily studied with experimental techniques. Hence, conducting a computational study of these systems can be helpful and be complementary with experimental work to elucidate their mechanisms. Thus, we have implemented the coarse-grained force field for proteins (COFFDROP) in Browndye 2.0 to study IDPs using Brownian dynamics (BD) simulations, which are often used to study large-scale motions with longer time scales and diffusion-limited molecular associations. Specifically, we have checked our COFFDROP implementation with eight naturally occurring IDPs and have investigated five (Glu-Lys)25 IDP sequence variants. From measuring the hydrodynamic radii of eight naturally occurring IDPs, we found the ideal scaling factor of 0.786 for non-bonded interactions. We have also measured the entanglement indices (average Cα distances to the other chain) between two (Glu-Lys) 25 IDP sequence variants, a property related to molecular association. We found that entanglement indices decrease for all possible pairs at excess salt concentration, which is consistent with long-range interactions of these IDP sequence variants getting weaker at increasing salt concentration.
Architecture and self-assembly of the jumbo bacteriophage nuclear shellLaughlin, T.G., A. Deep, A.M. Prichard, C. Seitz Y. Gu, E. Enustun, S. Suslov, K. Khanna1, E.A. Birkholz, E. Armbruster, J.A. McCammon, R.E. Amaro, J. Pogliano, K.D. Corbett, E. VillaNature (2022)    
Bacteria encode myriad defenses that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR/Cas systems. In response, one family of large bacteriophage employs a nucleus-like compartment to protect their replicating genomes by excluding host defense factors. However, the principle composition and structure of this compartment remain unknown. Here, we find that the bacteriophage nuclear shell assembles primarily from one protein, termed chimallin. Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin cooperatively self-assembles as a flexible sheet into closed micron-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
The essential role of loop dynamics in type II NRPS biomolecular recognitionCorpuz, J.C., A. Patel, T.D. Davis, L.M. Podust, J.A. McCammon, M.D. BurkartACS Chemical Biology in press (2022)    
Stomatal CO2/bicarbonate Sensor Consists of Two Interacting Protein Kinases, Raf-like HT1 and non-kinase-activity requiring MPK12/MPK4Takahashi Y., K. Bosmans, P.-K Hsu, K. Paul, C.-Y. Yeh, Y.-S. Wang, D. Yarmolinsky, M. Sierla, T. Vahisalu, C. Seitz, J.A. McCammon, J. Kangasjarvi, H. Kollist, L. Zhang, T. Trac, J.I. Schroeder.Science Advances in press (2022)    
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