Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations.

The SNAP receptor (SNARE) proteins syntaxin-1, SNAP-25, and synaptobrevin mediate neurotransmitter release by forming tight SNARE complexes that fuse synaptic vesicles with the plasma membranes in microseconds. Membrane fusion is generally explained by the action of proteins on macroscopic membrane properties such as curvature, elastic modulus, and tension, and a widespread model envisions that the SNARE motifs, juxtamembrane linkers, and C-terminal transmembrane regions of synaptobrevin and syntaxin-1 form continuous helices that act mechanically as semirigid rods, squeezing the membranes together as they assemble ("zipper") from the N to the C termini. However, the mechanism underlying fast SNARE-induced membrane fusion remains unknown. We have used all-atom molecular dynamics simulations to investigate this mechanism. Our results need to be interpreted with caution because of the limited number and length of the simulations, but they suggest a model of membrane fusion that has a natural physicochemical basis, emphasizes local molecular events over general membrane properties, and explains extensive experimental data. In this model, the central event that initiates fast (microsecond scale) membrane fusion occurs when the SNARE helices zipper into the juxtamembrane linkers which, together with the adjacent transmembrane regions, promote encounters of acyl chains from both bilayers at the polar interface. The resulting hydrophobic nucleus rapidly expands into stalk-like structures that gradually progress to form a fusion pore, aided by the SNARE transmembrane regions and without clearly discernible intermediates. The propensity of polyunsaturated lipids to participate in encounters that initiate fusion suggests that these lipids may be important for the high speed of neurotransmitter release.

Hairpin trimer transition state of amyloid fibril.

Protein fibril self-assembly is a universal transition implicated in neurodegenerative diseases. Although fibril structure/growth are well characterized, fibril nucleation is poorly understood. Here, we use a computational-experimental approach to resolve fibril nucleation. We show that monomer hairpin content quantified from molecular dynamics simulations is predictive of experimental fibril formation kinetics across a tau motif mutant library. Hairpin trimers are predicted to be fibril transition states; one hairpin spontaneously converts into the cross-beta conformation, templating subsequent fibril growth. We designed a disulfide-linked dimer mimicking the transition state that catalyzes fibril formation, measured by ThT fluorescence and TEM, of wild-type motif - which does not normally fibrillize. A dimer compatible with extended conformations but not the transition-state fails to nucleate fibril at any concentration. Tau repeat domain simulations show how long-range interactions sequester this motif in a mutation-dependent manner. This work implies that different fibril morphologies could arise from disease-dependent hairpin seeding from different loci.

SAMHD1 impairs type I interferon induction through the MAVS, IKKε, and IRF7 signaling axis during viral infection.

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) restricts human immunodeficiency virus type 1 (HIV-1) infection by reducing the intracellular dNTP pool. We have shown that SAMHD1 suppresses nuclear factor kappa-B activation and type I interferon (IFN-I) induction by viral infection and inflammatory stimuli. However, the mechanism by which SAMHD1 inhibits IFN-I remains unclear. Here, we show that SAMHD1 inhibits IFN-I activation induced by the mitochondrial antiviral-signaling protein (MAVS). SAMHD1 interacted with MAVS and suppressed MAVS aggregation in response to Sendai virus infection in human monocytic THP-1 cells. This resulted in increased phosphorylation of TANK binding kinase 1 (TBK1), inhibitor of nuclear factor kappa-B kinase epsilon (IKKε), and IFN regulatory factor 3 (IRF3). SAMHD1 suppressed IFN-I activation induced by IKKε and prevented IRF7 binding to the kinase domain of IKKε. We found that SAMHD1 interaction with the inhibitory domain (ID) of IRF7 (IRF7-ID) was necessary and sufficient for SAMHD1 suppression of IRF7-mediated IFN-I activation in HEK293T cells. Computational docking and molecular dynamics simulations revealed possible binding sites between IRF7-ID and full-length SAMHD1. Individual substitution of F411, E416, or V460 in IRF7-ID significantly reduced IRF7 transactivation activity and SAMHD1 binding. Furthermore, we investigated the role of SAMHD1 inhibition of IRF7-mediated IFN-I induction during HIV-1 infection. We found that THP-1 cells lacking IRF7 expression had reduced HIV-1 infection and viral transcription compared to control cells, indicating a positive role of IRF7 in HIV-1 infection. Our findings suggest that SAMHD1 suppresses IFN-I induction through the MAVS, IKKε, and IRF7 signaling axis.

Protein aggregates thermodynamically order regardless of sequence.

Proteins can aggregate into disordered aggregates or ordered assemblies such as amyloid fibrils. These two distinct phases serve differing roles in function and disease. How protein sequence determines the preferred phase is unknown. Here we establish a statistical mechanical disorder-to-order transition condition for compact polymer aggregates, including proteins. The theory produces a simple universal equation determining the favored phase as a function of temperature, polymer length, and interaction energy variance. We show that the sequence-dependent energy variance is efficiently calculated using atomistic simulations, so that the theory has no adjustable parameters. The equation accurately predicts experimental length-dependent crystallization temperatures of synthetic polymers. The equation also predicts that all protein sequences that aggregate will also favor ordering. Consequently, energy must be expended to maintain the steady-state disordered phase if it is not kinetically metastable on physiological timescales. More broadly, the theory suggests that aggregates of organic polymers will generally tend to order on habitable planets.

All-atom molecular dynamics simulations of Synaptotagmin-SNARE-complexin complexes bridging a vesicle and a flat lipid bilayer.

Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to Synaptotagmin-1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Synaptotagmin-1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics simulations of systems containing trans-SNARE complexes between two flat bilayers or a vesicle and a flat bilayer with or without fragments of Synaptotagmin-1 and/or complexin-1. Our results need to be interpreted with caution because of the limited simulation times and the absence of key components, but suggest mechanistic features that may control release and help visualize potential states of the primed Synaptotagmin-1-SNARE-complexin-1 complex. The simulations suggest that SNAREs alone induce formation of extended membrane-membrane contact interfaces that may fuse slowly, and that the primed state contains macromolecular assemblies of trans-SNARE complexes bound to the Synaptotagmin-1 C2B domain and complexin-1 in a spring-loaded configuration that prevents premature membrane merger and formation of extended interfaces, but keeps the system ready for fast fusion upon Ca2+ influx.

Control of neurotransmitter release by two distinct membrane-binding faces of the Munc13-1 C1C2B region.

Munc13-1 plays a central role in neurotransmitter release through its conserved C-terminal region, which includes a diacyglycerol (DAG)-binding C1 domain, a Ca2+/PIP2-binding C2B domain, a MUN domain and a C2C domain. Munc13-1 was proposed to bridge synaptic vesicles to the plasma membrane through distinct interactions of the C1C2B region with the plasma membrane: (i) one involving a polybasic face that is expected to yield a perpendicular orientation of Munc13-1 and hinder release; and (ii) another involving the DAG-Ca2+-PIP2-binding face that is predicted to result in a slanted orientation and facilitate release. Here, we have tested this model and investigated the role of the C1C2B region in neurotransmitter release. We find that K603E or R769E point mutations in the polybasic face severely impair Ca2+-independent liposome bridging and fusion in in vitro reconstitution assays, and synaptic vesicle priming in primary murine hippocampal cultures. A K720E mutation in the polybasic face and a K706E mutation in the C2B domain Ca2+-binding loops have milder effects in reconstitution assays and do not affect vesicle priming, but enhance or impair Ca2+-evoked release, respectively. The phenotypes caused by combining these mutations are dominated by the K603E and R769E mutations. Our results show that the C1-C2B region of Munc13-1 plays a central role in vesicle priming and support the notion that two distinct faces of this region control neurotransmitter release and short-term presynaptic plasticity.

TRIM7 inhibits enterovirus replication and promotes emergence of a viral variant with increased pathogenicity.

To control viral infection, vertebrates rely on both inducible interferon responses and less well-characterized cell-intrinsic responses composed of "at the ready" antiviral effector proteins. Here, we show that E3 ubiquitin ligase TRIM7 is a cell-intrinsic antiviral effector that restricts multiple human enteroviruses by targeting viral 2BC, a membrane remodeling protein, for ubiquitination and proteasome-dependent degradation. Selective pressure exerted by TRIM7 results in emergence of a TRIM7-resistant coxsackievirus with a single point mutation in the viral 2C ATPase/helicase. In cultured cells, the mutation helps the virus evade TRIM7 but impairs optimal viral replication, and this correlates with a hyperactive and structurally plastic 2C ATPase. Unexpectedly, the TRIM7-resistant virus has a replication advantage in mice and causes lethal pancreatitis. These findings reveal a unique mechanism for targeting enterovirus replication and provide molecular insight into the benefits and trade-offs of viral evolution imposed by a host restriction factor.

Tau local structure shields an amyloid-forming motif and controls aggregation propensity.

Tauopathies are neurodegenerative diseases characterized by intracellular amyloid deposits of tau protein. Missense mutations in the tau gene (MAPT) correlate with aggregation propensity and cause dominantly inherited tauopathies, but their biophysical mechanism driving amyloid formation is poorly understood. Many disease-associated mutations localize within tau's repeat domain at inter-repeat interfaces proximal to amyloidogenic sequences, such as 306VQIVYK311. We use cross-linking mass spectrometry, recombinant protein and synthetic peptide systems, in silico modeling, and cell models to conclude that the aggregation-prone 306VQIVYK311 motif forms metastable compact structures with its upstream sequence that modulates aggregation propensity. We report that disease-associated mutations, isomerization of a critical proline, or alternative splicing are all sufficient to destabilize this local structure and trigger spontaneous aggregation. These findings provide a biophysical framework to explain the basis of early conformational changes that may underlie genetic and sporadic tau pathogenesis.

Insights from simulations into the mechanism of human topoisomerase I: explanation for a seeming controversy in experiments.

Human topoisomerase-I is a vital enzyme involved in cellular regulation of DNA supercoiling. We extend our previous work on wild type enzyme [13] to study how different enzyme mutants with various parts of the protein clamped by disulfide mutations affect DNA rotation. Three different mutants have been simulated; they are clamped enzyme-DNA systems in which the disulfide bridge is formed by replacing His367 and Ala499, Gly365 and Ser534, and, respectively, Leu429 and Lys436 with Cys pairs. The first of these mutants, a 'distally clamped' enzyme, mimics the experimental study of Carey et al. [11], which reports DNA rotation within the clamped enzyme. The second one, a 'proximal clamp', mimics the study of Woo et al. [12], who do not observe DNA rotation. The third is a newly suggested mutant that clamps the hinge for protein opening; we use it to test a hypothesis on negative supercoil relaxation. Our simulations show that the helical domain α5 totally melts in relaxation of positive supercoils when the enzyme is proximally clamped, while it preserves its structure very well within the distally clamped one. Moreover, a distally clamped protein permits DNA rotations in both directions, while the proximal clamp allows rotations only for negatively supercoiled DNA. These observations reconcile the two seemingly contradictory experimental findings, suggesting that subtle changes in the location of the disulfide bridge alter the mechanism significantly.

Effect of substituents on spin density in benzimidazole nitronyl nitroxide radicals studied by electron spin resonance.

Several novel benzimidazole-3-oxide-1-oxyl radicals with substituents at 5 and/or 6 position were synthesized. The ESR analysis of nitrogen hyperfine coupling constants (hfccs) revealed that substituents at 5 and 6-position affect the spin density to greater extent than substituents on the phenyl ring at 2-position. Density functional theory calculations of nitrogen hfccs were performed using several different Pople type basis sets, as well as double and triple zeta quality individual gauge for localized orbital (IGLO-II, IGLO-III) and electron paramagnetic resonance (EPR-II, EPR-II) basis sets. Experimental and theoretical hfccs are compared.

Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation.

Topoisomerases are enzymes of quintessence to the upkeep of superhelical DNA, and are vital for replication, transcription and recombination. An atomic-resolution model for human topoisomerase I in covalent complex with DNA is simulated using molecular dynamics with external potentials that mimic torque and bias the DNA duplex downstream of a single-strand cut to rotate around the intact strand, according to the prevailing enzymatic mechanism. The simulations reveal the first dynamical picture of how topoisomerase accommodates large-scale motion of DNA as it changes its supercoiling state, and indicate that relaxation of positive and negative supercoils are fundamentally different. To relax positive supercoils, two separate domains (the 'lips') of the protein open up by about 10-14 A, whereas to relax negative supercoils, a continuous loop connecting the upper and lower parts (and which was a hinge for opening the lips) stretches about 12 A while the lips remain unseparated. Normal mode analysis is additionally used to characterize the functional flexibility of the protein. Remarkably, the same combination of low-frequency eigenvectors exhibit the dominant contribution for both rotation mechanisms through a see-saw motion. The simulated mechanisms suggest mutations to control the relaxation of either type of supercoiling selectively and advance a hypothesis for the debated role of the N-terminal domain in supercoil relaxation.

The singlet electronic ground state isomers of dialuminum monoxide: AlOAl, AlAlO, and the transition state connecting them.

The singlet electronic ground state isomers, X (1)Sigma(g) (+) (AlOAl D(infinityh)) and X (1)Sigma(+) (AlAlO C(infinitynu)), of dialuminum monoxide have been systematically investigated using ab initio electronic structure theory. The equilibrium structures and physical properties for the two molecules have been predicted employing self-consistent field (SCF) configuration interaction with single and double excitations (CISD), multireference CISD (MRCISD), coupled cluster with single and double excitations (CCSD), CCSD with perturbative triples [CCSD(T)], CCSD with iterative partial triple excitations (CCSDT-3 and CC3), and full triples (CCSDT) coupled cluster methods. Four correlation consistent polarized valence (cc-pVXZ) type basis sets were used. The AlAlO system is rather challenging theoretically. The two isomers are confirmed to have linear structures at all levels of theory. The symmetric isomer AlOAl is predicted to lie 81.9 kcal mol(-1) below the asymmetric isomer AlAlO at the cc-pV(Q+d)Z CCSD(T) level of theory. The predicted harmonic vibrational frequencies for the X (1)Sigma(g) (+) AlOAl molecule, omega(1)=517 cm(-1), omega(2)=95 cm(-1), and omega(3)=1014 cm(-1), are in good agreement with experimental values. The harmonic vibrational frequencies for the X (1)Sigma(+) AlAlO structure, omega(1)=1042 cm(-1), omega(2)=73 cm(-1), and omega(3)=253 cm(-1), presently have no experimental values with which to be compared. With the same methods the barrier heights for the isomerization AlOAl-->AlAlO and AlAlO-->AlOAl reactions were predicted to be 84.3 and 2.4 kcal mol(-1), respectively. The dissociation energies D(0) for AlOAl (X (1)Sigma(g) (+)) and AlAlO (X (1)Sigma(+))-->AlO (X (2)Sigma(+))+Al ((2)P) were determined to be 130.8 and 48.9 kcal mol(-1), respectively. Thus, both symmetric AlOAl (X (1)Sigma(g) (+)) and asymmetric AlAlO (X (1)Sigma(+)) isomers are expected to be thermodynamically stable with respect to the dissociation into AlO (X (2)Sigma(+)) + Al ((2)P) and kinetically stable for the isomerization reaction (AlAlO-->AlOAl) at sufficiently low temperatures.

Mono- and dibridged isomers of Si2H3 and Si2H4: the true ground state global minima. Theory and experiment in concert.

Highly correlated ab initio coupled-cluster theories (e.g., CCSD(T), CCSDT) were applied on the ground electronic states of Si(2)H(3) and Si(2)H(4), with substantive basis sets. A total of 10 isomers, which include mono- and dibridged structures, were investigated. Scalar relativistic corrections and zero-point vibrational energy corrections were included to predict reliable energetics. For Si(2)H(3), we predict an unanticipated monobridged H(2)Si-H-Si-like structure (C(s), (2)A'') to be the lowest energy isomer, in constrast to previous studies which concluded that either H(3)Si-Si (C(s), (2)A'') or near-planar H(2)Si-SiH (C(1), (2)A) is the global minimum. Our results confirm that the disilene isomer, H(2)Si-SiH(2), is the lowest energy isomer for Si(2)H(4) and that it has a trans-bent structure (C(2)(h), (1)A(g)). In addition to the much studied silylsilylene, H(3)Si-SiH, we also find that a new monobridged isomer H(2)Si-H-SiH (C(1), (1)A, designated 2c) is a minimum on the potential energy surface and that it has comparable stability; both isomers are predicted to lie about 7 kcal/mol above disilene. By means of Fourier transform microwave spectroscopy of a supersonic molecular beam, the rotational spectrum of this novel Si(2)H(4) isomer has recently been measured in the laboratory, as has that of the planar H(2)Si-SiH radical. Harmonic vibrational frequencies as well as infrared intensities of all 10 isomers were determined at the cc-pVTZ CCSD(T) level.