Urea is ubiquitously used as a protein denaturant. To study the structure and energetics of aqueous urea solutions, we have carried out molecular dynamics simulations for a wide range of urea concentrations and temperatures. The hydrogen bonds between urea and water were found to be significantly weaker than those between water molecules, which drives urea self-aggregation due to the hydrophobic effect. From the reduction of the water exposed urea surface area, urea was found to exhibit an aggregation degree of ca. 20% at concentrations commonly used for protein denaturation. Structurally, three distinct urea pair conformations were identified and their populations were analyzed by translational and orientational pair distribution functions. Furthermore, urea was found to strengthen water structure in terms of hydrogen bond energies and population of solvation shells. Our findings are consistent with a direct interaction between urea and the protein as the main driving force for protein denaturation. As an additional, more indirect effect, urea was found to enhance water structure, which would suggest a weakening of the hydrophobic effect.

Multiconfigurational ab initio calculations and QM/MM molecular dynamics simulations of a photoexcited cytosine-guanine base pair in both gas phase and embedded in the DNA provide detailed structural and dynamical insights into the ultrafast radiationless deactivation mechanism. Photon absorption promotes transfer of a proton from the guanine to the cytosine. This proton transfer is followed by an efficient radiationless decay of the excited state via an extended conical intersection seam. The optimization of the conical intersection revealed that it has an unusual topology, in that there is only one degeneracy-lifting coordinate. This is the central mechanistic feature for the decay both in vacuo and in the DNA. Radiationless decay occurs along an extended hyperline nearly parallel to the proton-transfer coordinate, indicating the proton transfer itself is not directly responsible for the deactivation. The seam is displaced from the minimum energy proton-transfer path along a skeletal deformation of the bases. Decay can thus occur anywhere along the single proton-transfer coordinate, accounting for the remarkably short excited-state lifetime of the Watson-Crick base pair. In vacuo, decay occurs after a complete proton transfer, whereas in DNA, decay can also occur much earlier. The origin of this effect lies in the temporal electrostatic stabilization of dipole in the charge-transfer state in DNA.

A principal component analysis has been applied on equilibrium simulations of a beta-heptapeptide that shows reversible folding in a methanol solution. The analysis shows that the configurational space contains only three dense sub-states. These states of relatively low free energy correspond to the "native" left-handed helix, a partly helical intermediate, and a hairpin-like structure. The collection of unfolded conformations form a relatively diffuse cloud with little substructure. Internal hydrogen-bonding energies were found to correlate well with the degree of folding. The native helical structure folds from the N terminus; the transition from the major folding intermediate to the native helical structure involves the formation of the two most C-terminal backbone hydrogen bonds. A four-state Markov model was found to describe transition frequencies between the conformational states within error limits, indicating that memory-effects are negligible beyond the nanosecond time-scale. The dominant native state fluctuations were found to be very similar to unfolding motions, suggesting that unfolding pathways can be inferred from fluctuations in the native state. The low-dimensional essential subspace, describing 69% of the collective atomic fluctuations, was found to converge at time-scales of the order of one nanosecond at all temperatures investigated, whereas folding/unfolding takes place at significantly longer time-scales, even above the melting temperature.

This article reports the reduction of the chloride [PhC(NtBu) 2 ]GeCl with potassium in THF to afford the reddish crystals of [PhC(NtBu) 2 ] 2 Ge 2 (2). The molecule of 2 contains a Ge-Ge bond. The X-ray structure and DFT calculation indicate that the Ge-Ge bond possesses an unusual gauche-bent geometry. The Ge-Ge bond length in 2 is 2.570 Å, which is very close to the single Ge-Ge interaction (2.61 Å) but significantly longer than that for typical digermenes, R 2 GeGeR 2 (2.21-2.51 Å) and the two structurally characterized digermynes (2.2850 Å and 2.2060 Å), which proves that there is no multiple bond character in 2.

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The functional importance of large-scale motions and transitions of carbonmonoxy myoglobin (MbCO) conformational substates (CSs) has been studied by molecular dynamics (MD) and conformational flooding (CF) simulations. A flooding potential was constructed from an 800 ps MD trajectory of solvated MbCO to accelerate slower protein motions beyond the time scale of contemporary simulations. Two conformational transitions (tier-1 substates) resulting from seven principal molecular motions were assigned to the spectroscopic A 0 state (tier-0 substate) of MbCO, where His64 is solvated and not within the hydrophobic pocket binding site. The first computed conformational transition involves a distal pocket gate defined by the C and D helices and the interconnecting CD loop (residues 40-55). The gate-like motion is interpreted to regulate ligand access from the distal side of the heme. Simultaneously, a proximal pocket lever involving the F helix and surrounding EF and FG loops (residues 82-105) is found to shuttle the heme deep into the protein matrix (heme rmsd of 3.9 Å) as the distal pocket gate opened. The lever's effect on the heme motion is assumed to attract ligands into the heme pocket. The second major transition involves the compression and expansion of the cavity formed by the EF loop (residues 77-84) and the GH loop and H helix (residues 122-138). The motion is interpreted to modulate the hydrophobic pocket volume and regulate the ligand access from the proximal side of the heme. A third computed conformational transition was found to be a combination of the previous motions. For the first time, CF was applied in a series of room temperature simulations to accelerate molecular motions of the MbCO native fold and define the lower tier hierarchy of substate structure. The computed CSs and associated transitions coincide with previously suggested putative ligand escape pathways, and support a hierarchical description of protein dynamics and structure. A unified model that utilizes both mechanisms of distal His64 modulation (tier-0) and protein equilibrium fluctuations (tier-1) is presented to explain ligand diffusion in the MbCO dissociation reaction.

Biomolecular function is often performed through motions of subunits. Rotary motions, in particular, are essential for the function of many motor proteins. Rotary mechanisms have been demonstrated, e.g., for the Fo and F1 motors in F-ATP synthase, and for the bacterial flagellar motor.

Tubulin dimers associate longitudinally and laterally to form metastable microtubules (MTs). MT 1 disassembly is preceded by subtle structural changes in tubulin fueled by GTP hydrolysis. These 2 changes render the MT lattice unstable, but it is unclear how exactly they affect lattice energetics 3 and strain. We performed long-time atomistic simulations to interrogate the impacts of GTP 4 hydrolysis on tubulin lattice conformation, lateral inter-dimer interactions, and (non-)local lateral 5 coordination of dimer motions. The simulations suggest that most of the hydrolysis energy is 6 stored in the lattice in the form of longitudinal strain. While not significantly affecting lateral bond 7 stability, the stored elastic energy results in more strongly confined and correlated dynamics of 8 GDP-tubulins, thereby entropically destabilizing the MT lattice. 9 12 filamentous assemblies of αβ-tubulin dimers stacked head-to-tail in polar protofilaments (PFs) 13 and folded into hollow tubes via lateral interactions [1,2] (Fig. 1a). Each dimer binds two GTP 14 molecules of which only the one bound to β-tubulin is hydrolyzed in the MT lattice over time [3,4]. 15 This hydrolysis reaction is fundamental to MT dynamic instability [5], i.e. random switching 16 between phases of growth and shrinkage ( Fig. 1a). Remarkably, both slow assembly and rapid 17 disassembly of MTs -the latter termed catastrophe -are able to perform mechanical work because 18 each tubulin dimer is a storage of chemical energy [6][7][8]. 19 The switch from a relaxed 'curved' conformation of tubulin favored in solution to a higher-energy 20 'straight' one is inherent to MT assembly [9][10][11][12][13][14][15]. It allows growing MTs to recruit and temporarily 21 stabilize GTP-tubulin in the straight form, most likely due to the greater bending flexibility of PFs at intra-and inter-dimer interfaces [13,[16][17][18]. It is therefore conceivable that collapsing MTs 23 would follow a reverse pathway during disassembly; namely, they would release the conformational 24 tension stored in GDP-tubulins that lateral bonds can no longer counteract. However, due to 25 the system complexity and together with the inability of modern structural methods to directly 26 visualize all sequential steps in the GTPase cycle in the straight MT body at high resolutions, it is 27 still unknown exactly how and where the hydrolysis energy is converted to mechanical strain in the 28 lattice. 29Recent high-resolution cryo-EM studies have revealed, in line with the early finding [19], that 30 GTP hydrolysis triggers changes in α-tubulin, resulting in a subnanometer longitudinal lattice 31 compaction (Fig. 1b) [20-23]. Because by itself this global lattice rearrangement does not fully 32 indicate how it is linked to the strain accumulation at the single-dimer level, two competing scenarios 33 have been proposed [24]. According to the seam-centric or strain model of MT catastrophe [20-22], 34 1/17 the gradual build-up of longitudinal tension along the lattice upon GTP hydrolysis is the pri...