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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. This article is protected by copyright. All rights reserved.

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 help visualize potential states of the release machinery en route to fusion, and suggest mechanistic features that may control the speed of release. In particular, the simulations suggest that the primed state contains almost fully assembled trans-SNARE complexes bound to the synaptotagmin-1 C2B domain and complexin-1 in a spring-loaded configuration where interactions of the C2B domain with the plasma membrane orient complexin-1 toward the vesicle, avoiding premature membrane merger but keeping the system ready for fast fusion upon Ca2+ influx.

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.

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 in two different orientations mediated by distinct interactions of the C1C2B region with the plasma membrane: i) one involving a polybasic face that yields a perpendicular orientation of Munc13-1 and hinders release; and ii) another involving the DAG-Ca2+-PIP2-binding face that induces a slanted orientation and facilitates 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 synaptic vesicle priming in primary murine hippocampal cultures, and Ca2+-independent liposome bridging and fusion in in vitro reconstitution assays. 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 re-orientation of Munc13-1 controls neurotransmitter release and short-term presynaptic plasticity.

To control viral infection, vertebrates rely on both inducible interferon responses and less well characterized cell intrinsic responses comprised 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.

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. Using cross-linking mass spectrometry, intramolecular FRET, recombinant protein and synthetic peptide systems, in silico modeling, and cell models, we conclude that the aggregation prone 306VQIVYK311 motif forms metastable compact structures with the upstream sequence that modulates aggregation propensity. 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.

Spectroscopic properties of quinoline-7-carboxaldehyde (Q7C) have been studied in detail both experimentally and theoretically. The FT-IR (4000–50 cm−1), FT-Raman (4000–50 cm−1), dispersive-Raman (3500–50 cm−1), and UV–Vis (200–400 nm) spectra of Q7C were recorded at room temperature (25 °C). Geometry parameters, potential energy surface about C CH(O) bond, harmonic vibrational frequencies, IR and Raman intensities, UV–Vis spectrum, and thermodynamic characteristics (at 298.15 K) of Q7C were computed at Hartree–Fock (HF) and density functional B3LYP levels employing the 6-311++G(d,p) basis set. Frontier molecular orbitals, molecular electrostatic potential, and Mulliken charge analyses of Q7C have also been performed. Q7C has two stable conformers that are energetically very close to each other with slight preference to the conformer that has oxygen atom of the aldehyde away from the nitrogen atom of the quinoline.

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.

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 electronic ground state [Formula: see text] and first excited state (Ã2Σ+) of phosphaethyne cation (HCP+) have been systematically investigated using ab initio electronic structure theory. The total energies, geometries, rotational constants, dipole moments, harmonic vibrational frequencies, and parameters for Renner–Teller splittings were determined using self-consistent-field (SCF), configuration interaction with single and double excitations (CISD), coupled cluster (CC) with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], CC with single, double, and iterative partial triple excitations (CCSDT-3), and CC with single, double, and full triple excitations (CCSDT) methods and eight different basis sets. Some of the largest full triples coupled cluster computations to date are reported. Degenerate bending frequencies for the Ã2Σ+ state were determined using the equation-of-motion (EOM)-CCSD technique. The two states have been confirmed to have linear equilibrium structures. At the full CCSDT level of theory with the correlation-consistent polarized valence quadruple zeta (cc-pVQZ) basis set, the classical [Formula: see text] splitting ( T e value) is predicted to be 47.7 kcal/mol (2.07 eV, 16,700 cm-1) and the quantum mechanical splitting (T0 value) to be 48.1 kcal/mol (2.08 eV, 16,800 cm-1), which are in excellent agreement with the experimental values of T e = 47.77 kcal/mol (2.072 eV , 16,708 cm -1) and T0 = 47.94 kcal/mol (2.079 eV, 16,766 cm-1). The excitation energies predicted by the CCSDT-3 and CCSD(T) methods differ from the full triples CCSDT result by 0.38 and 0.45 kcal/mol, respectively. With the aug-cc-pVQZ CCSDT-3 method the Renner parameter and the averaged harmonic bending vibrational frequency are determined to be ∊= -0.0390 and [Formula: see text] for the ground state of HCP+, which are reasonably consistent with the experimental values of ∊=-0.0415 and [Formula: see text]. The predicted dipole moments are 1.30 Debye ([Formula: see text] state, polarity-hydrogen atom positive) and 0.06 Debye (Ã2Σ+ state, polarity-phosphorus atom positive).

The 3Σ− and 3Π states for the GeC and GeSi diatomics have been investigated at the highly correlated coupled-cluster levels of theory. Large basis sets [including TZ3P(2d,2f)+2diff, cc-pVQZ, and aug-cc-pVQZ] were employed in order to predict reliable values for the experimentally unknown spectroscopic properties. The ground states were confirmed to be the 3Π state for GeC and the 3Σ− state for GeSi. Advanced theoretical treatments such as inclusion of core-valence correlation, scalar relativity, and complete basis set extrapolations have been performed to determine accurate energetic properties. The dissociation energies (D0) of 91.4 kcal/mol and 72.9 kcal/mol have been predicted for the X 3Π state of GeC and X 3Σ− state of GeSi, respectively. It is observed that the theoretical value of 72.9 kcal/mol for GeSi is in very good agreement with the experimental value of 71±5 kcal/mol. However, the predicted dissociation energy for the X 3Π state of GeC is found to be 18 kcal/mol smaller than the mass spectrom...

The three lowest-lying electronic states, [Xtilde] 1Σ+, A 3II and A 1II, of the linear BBO molecule have been systematically investigated using ab initio electronic structure theory. The equilibrium structures and physical properties including dipole moments, vibrational frequencies and associated infrared intensities, Renner parameters and energetics for the three states of BBO have been determined employing SCF, CISD, CCSD and CCSD(T) levels of theory and a wide range of basis sets. The ground state of BBO presents a degenerate real bending frequency, while the A 3II and A 1II states show two distinct real bending frequencies due to the Renner-Teller interaction. The bending motion of the A 1II state was analysed using the equation-of-motion (EOM)-CCSD and EOM-CC3 techniques in order to avoid possible variational collapse to a lower-lying state. The [Xtilde] 1Σ+-A 3II separation was predicted to be T 0 = 16.6 kcal mol−1 (5800 cm−1, 0.719 eV) at the cc-pVQZ CCSD(T) level of theory. With the cc-pVQZ EOM-C...

MP2/6-31G**//MP2/6-31G**, PMP2/6-31G**//MP2/6-31G**, MP4/6-311G(3df,2p)//MP2/6-31G**, PMP4/6-311G(3df,2p)//MP2/6-31G** and CCSD(T)/6-311++G**//MP2/6-31G** calculations have been used to investigate the H-abstraction reaction from CH3OCH3 (DME) whereas MP2/6-31G**//MP2/6-31G** and PMP2/6-31G**//MP2/6-31G** levels have been used to model the H-abstraction reaction from (CH3)3COCH3 (MTBE) by ˙OH. The methodology used has been proved to be adequate to reproduce the experimental geometrical parameters for the reactants and the C–H bond energies. The reaction rate constants for DME, calculated using the transition state theory reproduce the reported experimental results. The fact that H-abstraction is favored from the methoxy group of MTBE in comparison to the tert-butyl group has also been reproduced.

The X 2Π and A 2Σ+ states of the germanium methylidyne radical (HCGe) have been investigated at the SCF, CISD, CCSD, and CCSD(T) levels of theory. The total energies, equilibrium geometries, dipole moments, harmonic vibrational frequencies, infrared intensities, and Renner–Teller splitting are reported. The relativistic one-electron Darwin and mass-velocity terms are calculated using first-order perturbation theory and the effects of these corrections on energetics, harmonic vibrational frequencies, and Renner–Teller splitting are discussed. At our highest level of theory [CCSD(T)/cc-pVQZ], the ground electronic state (X 2Π) has a linear geometry with re(CH)=1.079 A and re(CGe)=1.769 A, in good agreement with the experimental values of r0(CH)=1.067 A and r0(CGe)=1.776 A. In the electronically excited A 2Σ+ state, HCGe is also found to have a linear geometry with re(CH)=1.074 A and a much shorter re(CGe)=1.669 A at the [CCSD(T)/cc-pVQZ] level, in agreement with experimental values of r0(CH)=1.059 A, r0(C...

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 alpha 5 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. (C) 2013 Elsevier Inc. All rights reserved.

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.

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.

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.

The rotational spectrum of a new monobridged isomer of Si(2)H(4), denoted here as H(2)Si(H)SiH, has been detected by Fourier transform microwave spectroscopy of a supersonic molecular beam through the discharge products of silane. On the basis of high-level coupled cluster theory, this isomer is calculated to lie only 7 kcalmol above disilene (H(2)SiSiH(2)), the most stable isomeric arrangement of Si(2)H(4), and to be fairly polar, with a calculated dipole moment of mu = 1.14 D. The rotational spectrum of H(2)Si(H)SiH exhibits closely spaced line doubling, characteristic of a molecule undergoing high-frequency inversion. Transition state calculations indicate that inversion probably occurs in two steps: migration of the bridged hydrogen atom to form silylsilylene, H(3)SiSiH, and then internal rotation of the SiH(3) group, followed by the reverse process. The potential energy surface for this type of inversion is quite shallow, with a barrier height of only 2-3 kcalmol. Searches for the rotational lines of silylsilylene, calculated to be of comparable stability to H(2)Si(H)SiH but about five times less polar (mu = 0.23 D), have also been undertaken, so far without success, even though strong lines of H(2)Si(H)SiH have been detected. The favorable energetics and high polarity of monobridged Si(2)H(4) with respect to either disilene or silylsilylene make it a plausible candidate for radioastronomical detection in sources such as IRC + 10216, where comparably large silicon molecules such as SiS, SiC(3), and SiC(4) have already been discovered.

The singlet-state potential energy surface of the disilaethynyl anion (Si2H−) has been investigated using ab initio self-consistent-field (SCF), configuration interaction with single and double excitations (CISD), coupled cluster with single and double excitations (CCSD), and CCSD with perturbative triple excitations [CCSD(T)] levels of theory with large basis sets. Four stationary points [cyclic (monobridged) 1A1 (C2v), linear 1Σ+ (C∞v), bent 1A′ (Cs), and quasilinear 1A′ (Cs) structures] were located with the correlated wave functions, while only two stationary points [cyclic (monobridged) 1A1 (C2v) and linear 1Σ+ (C∞v) structures] were found with the SCF method. The cyclic structure (C2v) is predicted to be the global minimum at all levels of theory. The linear structure (C∞v) is found to be a transition state between the two quasilinear structures (Cs) at the correlated levels of theory, while the SCF linear structure is predicted to be a transition state between the two cyclic structures. The quasili...

The electronic structures of the ground and lowest lying excited state of the silicon methylidyne radical (HCSi) have been investigated at the self-consistent field, configuration interaction with single and double excitations, coupled cluster with single and double excitations (CCSD), and CCSD including a perturbative expansion for connected triples CCSD(T) levels of theory with a wide range of basis sets. The total energies and physical properties including equilibrium geometries, dipole moments, harmonic vibrational frequencies, and Renner–Teller splitting are reported. At our highest level of theory [CCSD(T)/cc-pVQZ], the ground electronic state (X 2Π) has a linear geometry with re(CH)=1.0781 A and re(CSi)=1.6956 A. This is in good agreement with the experimental values of r0(CH)=1.0677 A and r0(CSi)=1.6925 A, respectively. In the A 2Σ+ state, HCSi is also found to have a linear geometry with re(CH)=1.0737 A and re(CSi)=1.6130 A at the [CCSD(T)/cc-pVQZ] level, confirming experimental values of r0(CH)...