Multiconfigurational Coarse-Grained Molecular Dynamics.

Standard low resolution coarse-grained modeling techniques have difficulty capturing multiple configurations of protein systems. Here, we present a method for creating accurate coarse-grained (CG) models with multiple configurations using a linear combination of functions or "states". Individual CG models are created to capture the individual states, and the approximate coupling between the two states is determined from an all-atom potential of mean force. We show that the resulting multiconfiguration coarse-graining (MCCG) method accurately captures the transition state as well as the free energy between the two states. We have tested this method on the folding of dodecaalanine, as well as the amphipathic helix of endophilin.

Emerging ß-Sheet Rich Conformations in Supercompact Huntingtin Exon-1 Mutant Structures.

There exists strong correlation between the extended polyglutamines (polyQ) within exon-1 of Huntingtin protein (Htt) and age onset of Huntington's disease (HD); however, the underlying molecular mechanism is still poorly understood. Here we apply extensive molecular dynamics simulations to study the folding of Htt-exon-1 across five different polyQ-lengths. We find an increase in secondary structure motifs at longer Q-lengths, including ß-sheet content that seems to contribute to the formation of increasingly compact structures. More strikingly, these longer Q-lengths adopt supercompact structures as evidenced by a surprisingly small power-law scaling exponent (0.22) between the radius-of-gyration and Q-length that is substantially below expected values for compact globule structures (∼0.33) and unstructured proteins (∼0.50). Hydrogen bond analyses further revealed that the supercompact behavior of polyQ is mainly due to the "glue-like" behavior of glutamine's side chains with significantly more side chain-side chain H-bonds than regular proteins in the Protein Data Bank (PDB). The orientation of the glutamine side chains also tend to be "buried" inside, explaining why polyQ domains are insoluble on their own.

Molecular Mechanism of Stabilizing the Helical Structure of Huntingtin N17 in a Micellar Environment.

Huntington's disease is a deadly neurodegenerative disease caused by the fibrilization of huntingtin (HTT) exon-1 protein mutants. Despite extensive efforts over the past decade, much remains unknown about the structures of (mutant) HTT exon-1 and their enigmatic roles in aggregation. Particularly, whether the first 17 residues in the N-terminal (HTT-N17) adopt a helical or a coiled structure remains unclear. Here, with the rigorous study of molecular dynamics simulations, we explored the most possible structures of HTT-N17 in both dodecylphosphocholine (DPC) micelles and aqueous solution, using three commonly applied force fields (OPLS-AA/L, CHARMM36, and AMBER99sb*-ILDNP) to examine the underlying molecular mechanisms and rule out potential artifacts. We show that local environments are essential for determining the secondary structure of HTT-N17. This is evidenced by the insertion of five hydrophobic residues of HTT-N17 into the DPC micelle, which promotes the formation of an amphipathic helix, whereas such amphipathic helices unfold quickly in aqueous solution. A relatively low free-energy barrier (∼3 kcal/mol) for the secondary structure transformation was also observed for all three force fields from their respective folding-free-energy landscapes, which accounts for possible HTT-N17 conformational changes upon environmental shifts such as membrane binding and protein complex aggregation.

Experimental determination of redox cooperativity and electronic structures in catalytically active Cu-Fe and Zn-Fe heterobimetallic complexes.

Complexes of the type (NHC)M-Fp (NHC = N-heterocyclic carbene, M = Cu or ZnCl, Fp = FeCp(CO)2) have been used recently as replacements for noble metal C-H functionalization catalysts and for small molecule activation studies. The promising reactivity of these systems has been linked to the use of the late metal electrophiles Cu and Zn in place of early metal electrophiles, and also to the ability of the M-Fe pairs to cooperate during catalytically relevant multielectron redox processes such as bimetallic oxidative addition and bimetallic reductive elimination. Using Mössbauer spectroscopy and metal K-edge XANES analysis, a detailed electronic structure description of these complexes is presented. One unusual feature of the late-metal M-Fp interactions is the presence of significant M → Fe π-backdonation in addition to Fe → M σ-donation; this π-backdonation is absent in early metal analogues and is apparent from analysis of Mössbauer data and Fe K-edge data. Multi-edge XANES analysis of C-I bimetallic oxidative addition at a Cu-Fe reaction center reveals little change in metal effective nuclear charges during the two-electron redox process. IR spectroscopy indicates that the supporting carbonyl ligands participate to a large extent in the redox process.

The entropic origin of solvent effects on the single bond cZt-tZt isomerization rate constant of 1,3,5-cis-hexatriene in alkane and alcohol solvents: a molecular dynamics study.

The single-bond cZt-tZt isomerization rate constants of 1,3,5-cis-hexatriene dissolved in a series of explicit alkane (cyclohexane, n-heptane, and cycloheptane) and alcohol (methanol, ethanol, and n-propanol) solvents were calculated via reactive flux theory, from classical molecular dynamics simulations, at different temperatures (275-325 K). We find that the isomerization rate constants in alcohol solvents are slower than those in alkane solvents, in accord with the observed experimental trend (Harris, D. A.; Orozco, M. B.; Sension, R. J. J. Phys. Chem. A 2006, 110, 9325-9333). We also find that the same trend is obtained when the transition state theory limit of the reactive flux expression for the reaction rate constant is employed. The solvent dependence of the reaction rate constant is then traced back to the fundamentally different structure of the solvation shell in alcohol and alkane solvents. Whereas in alcohol solvents, hexatriene fits inside a rigid cavity formed by the hydrogen-bonded network, which is relatively insensitive to conformational dynamics, alkane solvents form a cavity around hexatriene that adjusts to the conformational state of hexatriene, thereby increasing the entropy of transition state configurations relative to reactant configurations and giving rise to faster isomerization.

Loss of the F-BAR protein CIP4 reduces platelet production by impairing membrane-cytoskeleton remodeling.

Megakaryocytes generate platelets through extensive reorganization of the cytoskeleton and plasma membrane. Cdc42 interacting protein 4 (CIP4) is an F-BAR protein that localizes to membrane phospholipids through its BAR domain and interacts with Wiskott-Aldrich Syndrome Protein (WASP) via its SRC homology 3 domain. F-BAR proteins promote actin polymerization and membrane tubulation. To study its function, we generated CIP4-null mice that displayed thrombocytopenia similar to that of WAS(-) mice. The number of megakaryocytes and their progenitors was not affected. However, the number of proplatelet protrusions was reduced in CIP4-null, but not WAS(-), megakaryocytes. Electron micrographs of CIP4-null megakaryocytes showed an altered demarcation membrane system. Silencing of CIP4, not WASP, expression resulted in fewer proplatelet-like extensions. Fluorescence anisotropy studies showed that loss of CIP4 resulted in a more rigid membrane. Micropipette aspiration demonstrated decreased cortical actin tension in megakaryocytic cells with reduced CIP4 or WASP protein. These studies support a new biophysical mechanism for platelet biogenesis whereby CIP4 enhances the complex, dynamic reorganization of the plasma membrane (WASP independent) and actin cortex network (as known for WASP and cortical actin) to reduce the work required for generating proplatelets. CIP4 is a new component in the highly coordinated system of megakaryocytic membrane and cytoskeletal remodeling affecting platelet production.

Autoinhibition of endophilin in solution via interdomain interactions.

Endophilin is a key protein involved in clathrin-mediated endocytosis. Previous computational and experimental work suggested that the N-terminal helix is embedded into the membrane to induce curvature; however, the role of the SH3 domain remains controversial. To address this issue, we performed computer simulations of the endophilin dimer in solution to understand the interaction between the N-BAR and SH3 domains and its effect on biological function. We predict that the helix binds to the SH3 domain through hydrophobic and salt-bridge interactions. This protects the hydrophobic residues on both domains and keeps the SH3 domain near the end of the N-BAR domain, in agreement with previous experimental results. The complex has a binding strength similar to a few hydrogen bonds (13.0 ± 0.6 kcal/mol), and the SH3 domain stabilizes the structure of the N-terminal helix in solution. Electrostatic calculations show a large region of strongly positive electrostatic potential near the N-terminal that can orient the helix toward the membrane and likely embed the helix into the membrane surface. This predicted mechanism suggests that endophilin can select for both curvature and electrostatic potential when interacting with membranes, highlighting the importance of the SH3 domain in regulating the function of endophilin.

Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling.

Endophilin N-BAR (N-terminal helix and Bin/amphiphysin/Rvs) domain tubulates and vesiculates lipid membranes in vitro via its crescent-shaped dimer and four amphipathic helices that penetrate into membranes as wedges. Like F-BAR domains, endophilin N-BAR also forms a scaffold on membrane tubes. Unlike F-BARs, endophilin N-BARs have N-terminal H0 amphipathic helices that are proposed to interact with other N-BARs in oligomer lattices. Recent cryo-electron microscopy reconstructions shed light on the organization of the N-BAR lattice coats on a nanometer scale. However, because of the resolution of the reconstructions, the precise positioning of the amphipathic helices is still ambiguous. In this work, we applied a coarse-grained model to study various membrane remodeling scenarios induced by endophilin N-BARs. We found that H0 helices of N-BARs prefer to align in an antiparallel manner at two ends of the protein to form a stable lattice. The deletion of H0 helices causes disruption of the lattice. In addition, we analyzed the persistence lengths of the protein-coated tubes and found that the stiffness of endophilin N-BAR-coated tubules qualitatively agrees with previous experimental work studying N-BAR-coated tubules. Large-scale simulations on membrane liposomes revealed a systematic relation between H0 helix density and local membrane curvature fluctuations. The data also suggest that the H0 helix is required for BARs to form organized structures on the liposome, further illustrating its important function.

Vibrational energy relaxation in liquid HCl and DCl via the linearized semiclassical method: electrostriction versus quantum delocalization.

The rate constant for vibrational energy relaxation of the H-Cl stretch in liquid HCl (T = 188K, ρ = 19.671 nm(-3)) is calculated within the framework of the Landau-Teller formula. The force-force correlation function is calculated via the recently introduced force-derivative-free linearized semiclassical method [Vázquez et al. J. Phys. Chem. A2010, 114, 5682]. The calculated vibrational energy relaxation rate constant is found to be in excellent agreement with experiment, and the electrostatic force is found to contribute significantly to the high frequency component of the force-force correlation function. In contrast, the corresponding classical vibrational energy relaxation rate constant is found to be 2 orders of magnitude slower than the experimental value, and the classical force-force correlation function is found to be dominated by the Lennard-Jones forces. These observations suggest that quantum delocalization, enhanced by the light mass of hydrogen, amplifies the contribution of repulsive Coulombic forces to the force-force correlation function, thereby making electrostriction an unlikely mechanism for vibrational energy relaxation in the case of hydrogen stretches. This interpretation is reinforced by the results of a similar calculation in the case of the D-Cl stretch in liquid DCl under the same conditions. In this case, the quantum enhancement of the vibrational energy relaxation rate constant is observed to be greatly diminished in comparison to HCl, thereby giving rise to a reversal of the isotope effect in comparison to that predicted by the corresponding classical treatment (i.e., whereas the classical vibrational energy relaxation rate of DCl is faster than that of HCl, the opposite trend is predicted by the linearized semiclassical treatment). It is also shown that the vibrational energy relaxation of DCl is completely dominated by the Lennard-Jones forces within either classical and semiclassical treatments, thereby suggesting that electrostriction is the underlying mechanism in this case.

Vibrational energy relaxation rates via the linearized semiclassical method without force derivatives.

A new computational scheme for calculating vibrational energy relaxation rate constants is presented that is based on applying the linearized semiclassical approximation to the symmetrized force-force correlation function. Unlike the previous scheme of Geva and Shi [Shi, Q.; Geva, E. J. Phys. Chem A 2003, 107, 9059], which was based on applying the linearized semiclassical approximation to the standard force-force correlation function, the new scheme does not involve a power expansion of the initial force in terms of the Wigner transform integration variable Delta and as a result is more accurate and does not require force derivatives as input. The main disadvantages of the new scheme are its slower convergence rate in comparison to the Shi-Geva scheme and its ambiguity with respect to the choice of configuration around which the local harmonic approximation is performed. The computational feasibility and accuracy of the new approach is demonstrated on a number of benchmark models, including the highly challenging case of nonpolar diatomic liquids. It is observed that performing the local harmonic approximation around the configuration used for computing the initial force yields the best agreement with experiment.