Characterizing atomic details of membrane binding of peripheral membrane proteins by molecular dynamics (MD) has been significantly hindered by the slow dynamics of membrane reorganization associated with the phenomena. To expedite lateral diffusion of lipid molecules without sacrificing the atomic details of such interactions, we have developed a novel membrane representation, to our knowledge, termed the highly mobile membrane-mimetic (HMMM) model to study binding and insertion of various molecular species into the membrane. The HMMM model takes advantage of an organic solvent layer to represent the hydrophobic core of the membrane and short-tailed phospholipids for the headgroup region. We demonstrate that using these components, bilayer structures are formed spontaneously and rapidly, regardless of the initial position and orientation of the lipids. In the HMMM membrane, lipid molecules exhibit one to two orders of magnitude enhancement in lateral diffusion. At the same time, the membrane atomic density profile of the headgroup region produced by the HMMM model is essentially identical to those obtained for full-membrane models, indicating the faithful representation of the membrane surface by the model. We demonstrate the efficiency of the model in capturing spontaneous binding and insertion of peripheral proteins by using the membrane anchor (γ-carboxyglutamic-acid-rich domain; GLA domain) of human coagulation factor VII as a test model. Achieving full insertion of the GLA domain consistently in 10 independent unbiased simulations within short simulation times clearly indicates the robustness of the HMMM model in capturing membrane association of peripheral proteins very efficiently and reproducibly. The HMMM model will provide significant improvements to the current all-atom models by accelerating lipid dynamics to examine protein-membrane interactions more efficiently.

Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochemistry. Because most practical photochemistry occurs in solution and protein environments, it is important to understand the role complex environments play in directing excited-state dynamics generally, as well as specific environmental effects on CI geometries and energies. In order to model such effects, we employ the full multiple spawning (FMS) method for multistate quantum dynamics, together with hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy surfaces using both semiempirical and ab initio QM methods. In this article, we present an overview of these methods, and a comparison of the excited-state dynamics of several biological chromophores in solvent and protein environments. Aqueous solvation increases the rate of quenching to the ground state for both the photoactive yellow protein (PYP) and green fluorescent protein (GFP) chromophores, apparently by energetic stabilization of their respective CIs. In contrast, solvation in methanol retards the quenching process of the retinal protonated Schiff base (RPSB), the rhodopsin chromophore. Protein environments serve to direct the excited-state dynamics, leading to higher quantum yields and enhanced reaction selectivity.

Recently developed bioinformatic tools have bolstered the discovery of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Using an improved version of Rapid ORF Description & Evaluation Online (RODEO 2.0), a biosynthetic gene cluster mining algorithm, we bioinformatically mapped the sactipeptide RiPP class via the radical S-adenosylmethionine (SAM) enzymes that form the characteristic sactionine (sulfur-to-alpha carbon) crosslinks between cysteine and acceptor residues. Hundreds of new sactipeptide biosynthetic gene clusters were uncovered and a novel sactipeptide "huazacin" with growth-suppressive activity against Listeria monocytogenes was characterized. Bioinformatic analysis further suggested that a group of sactipeptide-like peptides heretofore referred to as SCIFFs (six cysteines in forty-five residues) might not be sactipeptides as previously thought. Indeed, the bioinformatically-identified SCIFF

Many regulatory processes in biology involve reversible association of proteins with membranes. Clotting proteins bind to phosphatidylserine (PS) on cell surfaces, but a clear picture of this interaction has yet to emerge. We present a novel explanation for membrane binding by GLA domains of clotting proteins, supported by biochemical studies, solid-state NMR analyses, and molecular dynamics simulations. The model invokes a single “phospho-l-serine-specific” interaction and multiple “phosphate-specific” interactions. In the latter, the phosphates in phospholipids interact with tightly bound Ca2+ in GLA domains. We show that phospholipids with any headgroup other than choline strongly synergize with PS to enhance factor X activation. We propose that phosphatidylcholine and sphingomyelin (the major external phospholipids of healthy cells) are anticoagulant primarily because their bulky choline headgroups sterically hinder access to their phosphates. Following cell damage or activation, exposed PS and phosphatidylethanolamine collaborate to bind GLA domains by providing phospho-l-serine-specific and phosphate-specific interactions, respectively.