We have traditionally relied on extremely elevated temperatures (498 K, 225 8C) to investigate the unfolding process of proteins within the timescale available to molecular dynamics simulations with explicit solvent. However, recent advances in computer hardware have allowed us to extend our thermal denaturation studies to much lower temperatures. Here we describe the results of simulations of chymotrypsin inhibitor 2 at seven temperatures, ranging from 298 K to 498 K. The simulation lengths vary from 94 ns to 20 ns, for a total simulation time of 344 ns, or 0.34 ms. At 298 K, the protein is very stable over the full 50 ns simulation. At 348 K, corresponding to the experimentally observed melting temperature of CI2, the protein unfolds over the first 25 ns, explores partially unfolded conformations for 20 ns, and then refolds over the last 35 ns. Above its melting temperature, complete thermal denaturation occurs in an activated process. Early unfolding is characterized by sliding or breathing motions in the protein core, leading to an unfolding transition state with a weakened core and some loss of secondary structure. After the unfolding transition, the core contacts are rapidly lost as the protein passes on to the fully denatured ensemble. While the overall character and order of events in the unfolding process are well conserved across temperatures, there are substantial differences in the timescales over which these events take place. We conclude that 498 K simulations are suitable for elucidating the details of protein unfolding at a minimum of computational expense.

Hydration effects on the molecular structure and amide I mode frequency of a prototype peptide molecule, N-methylacetamide (NMA), when it is solvated by a few water molecules, were investigated by carrying out ab initio calculations for a number of NMA–water complexes. The harmonic frequency shift of the amide I mode in NMA–nD2O (n=1–5) complex was found to originate from the combination of the molecular cubic anharmonicity and displacement of the amide I coordinate when the NMA is hydrated. Using a multivariate least-square fitting method, the effective transition charges of six NMA sites were determined. A brief discussion on how this empirical model can be used to quantitatively describe solvatochromic frequency shift of the NMA amide I mode in solution is presented.

SummaryMulti-subunit SMC complexes control chromosome superstructure and promote chromosome disjunction, conceivably by actively translocating along DNA double helices. SMC subunits comprise an ABC ATPase “head” and a “hinge” dimerization domain connected by a 49 nm coiled-coil “arm.” The heads undergo ATP-dependent engagement and disengagement to drive SMC action on the chromosome. Here, we elucidate the architecture of prokaryotic Smc dimers by high-throughput cysteine cross-linking and crystallography. Co-alignment of the Smc arms tightly closes the interarm space and misaligns the Smc head domains at the end of the rod by close apposition of their ABC signature motifs. Sandwiching of ATP molecules between Smc heads requires them to substantially tilt and translate relative to each other, thereby opening up the Smc arms. We show that this mechanochemical gating reaction regulates chromosome targeting and propose a mechanism for DNA translocation based on the merging of DNA loops upon closure of Smc arms.

Ab initio calculations of the amide I modes of right-handed α -helical, 310-helical, left-handed α -helical, π-helical, parallel β-sheet, antiparallel β-sheet, and fully extended β-sheet polypeptide conformations with two to five peptide bonds were performed to investigate the site dependencies of the local amide I mode frequencies and vibrational coupling constants between neighboring peptides. A Hessian matrix reconstruction method is used to obtain these quantities from the ab initio-calculated amide I normal modes. The local amide I mode frequencies of the peptides in the inner region of a given helical polypeptide are significantly larger than those of terminal peptides, whereas the local amide I mode frequencies of β-sheet polypeptides are not site-dependent. The amide I vibrational coupling constants are not sensitive to the length of the polypeptide, but they are found to be strongly dependent on the three-dimensional conformation of the polypeptides. An empirical model for predicting diagonal amide I mode frequency shift is used to theoretically describe the site dependence of the local amide I mode frequency.

Articles you may be interested inAccurate ab initio quartic force fields for NH 2 − and CCH − and rovibrational spectroscopic constants for their isotopologs Amide I vibrational modes in glycine dipeptide analog: Ab initio calculation studiesThe local amide I mode frequency of a peptide has been found to be strongly affected by the interpeptide interaction, because the electronic and molecular structures of the peptide bond change due to the electrostatic interaction with surrounding peptides. Ab initio vibrational analyses of three different series of N-methylacetamide dimers and glycine dipeptide analog in ␣-helical and ␤-sheet conformations have been performed. It is found that the diagonal force constant shift originates from the electronic structure change of a given peptide in combination with the cubic anharmonicity of the local amide I mode.

Articles you may be interested inSingle-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling J. Chem. Phys. 137, 094301 (2012); 10.1063/1.4747507Accurate ab initio quartic force fields for NH 2 − and CCH − and rovibrational spectroscopic constants for their isotopologs Isotope effects in linear dihydrogen bonded complexes containing LiH

A series of eight thermal cheletropic decarbonylations show dramatic differences in reaction pathways and in activation energies depending on the molecular orbital topology, as calculated by using ab initio molecular orbital theory (MP2(FC)/6-31G* optimized geometries and MP4/D95** + ZPE single point energies). The decarbonylations of 3-cyclopentenone (1) and bicyclo[2.2.1]hepta-2,5-diene-7-one (3) are pericyclic, orbital symmetry allowed reactions, but it is argued that the decarbonylation of cyclopropanone (9), although formally orbital symmetry allowed, lacks an energy of concert and thus is “effectively forbidden”. The carbon monoxide produced from 1 is predicted to be formed vibrationally cool and rotationally hot. Fragmentations of 2,3-furandione (5) and 2,3-pyrroledione (7) are pseudopericyclic reactions with two orbital disconnections, proceed via planar transition structures, and have activation energies that are much lower than expected for pericyclic reactions of comparable exothermicity. It will be an experimental challenge to determine if the carbon monoxide product from each of these is formed with little vibrational or rotational excitation as predicted. Fragmentations of 3H-furan-2-one (11), 3-cyclopentene-1,2-dione (13), and 3-methylene-3H-furan-2-one (15) each have a single disconnection. Strong bonding at the orbital disconnection in the transition structure tends to lower the barrier and give the reaction more pseudopericyclic character.

Hydrophobicity is thought to underlie self-assembly in biological systems. However, the protein surface comprises hydrophobic and hydrophilic patches, and understanding the impact of such a chemical heterogeneity on protein self-assembly in water is of fundamental interest. Here, we report structural and thermodynamic investigations on the dimer formation of full-length amyloid-β proteins in water associated with Alzheimer's disease. Spontaneous dimerization process-from the individual diffusive regime at large separations, through the approach stage in which two proteins come close to each other, to the structural adjustment stage toward compact dimer formation-was captured in full atomic detail via unguided, explicit-water molecular dynamics simulations. The integral-equation theory of liquids was then applied to simulated protein structures to analyze hydration thermodynamic properties and the water-mediated interaction between proteins. We demonstrate that hydrophilic residues play a key role in initiating the dimerization process. A long-range hydration force of enthalpic origin acting on the hydrophilic residues provides the major thermodynamic force that drives two proteins to approach from a large separation to a contact distance. After two proteins make atomic contacts, the nature of the water-mediated interaction switches from a long-range enthalpic attraction to a shortrange entropic one. The latter acts both on the hydrophobic and hydrophilic residues. Along with the direct protein-protein interactions that lead to the formation of intermonomer hydrogen bonds and van der Waals contacts, the water-mediated attraction of entropic origin brings about structural adjustment of constituent monomer proteins toward the formation of a compact dimer structure.solvation thermodynamics | dehydration | protein interface W ater-mediated interaction such as hydrophobic interaction plays a key role in protein folding and protein self-assembly (1-3), yet elucidating its physical and chemical basis still remains a challenge. Recent theoretical advances in understanding the hydrophobic effect have elucidated that the hydrophobic inter action between small apolar groups is markedly different from that between large hydrophobic solutes, with the cross-over length-scale being of the order of 10 Å (see, e.g., refs. 4 and 5 for review). However, most of previous studies employed solutes such as cylinders, plates, or hydrophobic chains, and a direct applicability of findings therefrom to proteins is not obvious. A major obstacle here is the fact that protein surfaces are both topologically and chemically heterogeneous (6, 7): Protein surfaces are irregular in shape and hydrophobic residues are laced with hydrophilic ones. The main focus of the present work is to contribute to the understanding of the impact of chemical heterogeneity on protein self-assembly in water via the study of solvation for a realistic system of protein and water.Self-assembly of large hydrophobic solutes is thought to be driven by a drying transition ...