Price of disorder in the lac repressor hinge helix

The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.     

A Novel Phase of Li15Si4 Synthesized under Pressure

Li₁₅Si₄, the only crystalline phase that forms during lithiation of the Si anode in lithium‐ion batteries, is found to undergo a structural transition to a new phase at 7 GPa. Despite the large unit cell of Li₁₅Si₄ (152 atoms in the unit cell), ab initio evolutionary metadynamics (using the USPEX code) successfully predicts the atomic structure of this new phase (β‐Li₁₅Si₄), which has an orthorhombic structure with an Fdd2 space group. In the new β‐Li₁₅Si₄ phase Si atoms are isolated by Li atoms analogous to the original cubic phase (α‐Li₁₅Si₄), whereas the atomic packing is more efficient owing to the higher Si? Li coordination number and shorter Si? Li, Li? Li bonds. β‐Li₁₅Si₄ has substantially larger elastic moduli compared with α‐Li₁₅Si₄, and has a good electrical conductivity. As a result, β‐Li₁₅Si₄ has superior resistance to deformation and fracture under stress. The theoretical volume expansion of Si would decrease 25% if it transforms to β‐Li₁₅Si₄, instead of α‐Li₁₅Si₄, during lithiation. Moreover, β‐Li₁₅Si₄ can be recovered back to ambient pressure, providing opportunities to further investigate its properties and potential applications.     

Characterisation of the hydrophobic collapse of polystyrene in water using free energy techniques

We characterise the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained (CG) molecular simulation. We next explore the scaling behaviour of the collapsed globular shape at the minimum energy configuration, characterised by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behaviour of the solvent accessible surface area (SASA) as a function of chain length, finding a similar exponent for both all atomistic and CG simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths.     

Exploring the unbinding of Leishmania (L.) amazonensis CPB derived‐epitopes from H2 MHC class I proteins

New strategies to control Leishmania disease demand an extensive knowledge about several aspects of infection including the understanding of its molecular events. In murine models, cysteine proteinase B from Leishmania amazonensis promotes regulation of immune response, and fragments from its C‐terminus extension (cyspep) can play a decisive role in the host‐parasite interaction. The interaction between cyspep‐derived peptides and major histocompatibility complex (MHC) proteins is a crucial factor in Leishmania infections. Seven cyspep‐derived peptides, previously identified as capable of interacting with H‐2 (murine) MHC class I proteins, were studied in this work. We established a protocol to simulate the unbinding of these peptides from the cleft of H‐2 receptors. From the simulations, we estimated the corresponding free energy of dissociation (ΔG_d) and described the molecular events that occur during the exit of peptides from the cleft. To test the reliability of this method, we first applied it to a calibration set of four crystallographic MHC/peptide complexes. Next, we explored the unbinding of the seven complexes mentioned above. Results were consistent with ΔG_d values obtained from surface plasmon resonance (SPR) experiments. We also identified some of the primary interactions between peptides and H‐2 receptors, and we detected three regions of influence for the interaction. This pattern was systematically observed for the peptides and helped determine a minimum distance for the real interaction between peptides and H‐2 proteins occurring at ～25 Å. Proteins 2016; 84:473–487. © 2016 Wiley Periodicals, Inc.     

Refinement of protein-protein complexes in contact map space with metadynamics simulations

Accurate protein-protein complex prediction, to atomic detail, is a challenging problem. For flexible docking cases, current state-of-the-art docking methods are limited in their ability to exhaustively search the high dimensionality of the problem space. In this study, to obtain more accurate models, an investigation into the local optimization of initial docked solutions is presented with respect to a reference crystal structure. We show how physics-based refinement of protein-protein complexes in contact map space (CMS), within a metadynamics protocol, can be performed. The method uses 5 times replicated 10 ns simulations for sampling and ranks the generated conformational snapshots with ZRANK to identify an ensemble of n snapshots for final model building. Furthermore, we investigated whether the reconstructed free energy surface (FES), or a combination of both FES and ZRANK, referred to as CS_α, can help to reduce snapshot ranking error.     

CO escape from myoglobin with metadynamics simulations

The relatively small size of myoglobin makes it suitable for the investigation of the ligand escape process in respiratory proteins and, in general, an ideal model system for the study of the more general structure-function paradigm. In this work, we use Molecular Dynamics simulations combined with an accelerated algorithm, the metadynamics, to probe the escape of CO from myoglobin. Our approach permits to quantitatively describe the escape process via the reconstruction of the associated free energy surface. Additionally, hints on the involvement of a larger numbers of residues than hitherto assumed in the gating process are extracted from our data.     

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

With the help of molecular‐dynamics simulations, we studied the effect of urea and guanidine chloride on the thermodynamic and structural properties of the helical fragment of protein GB1, comparing them with those of its second beta hairpin. We showed that the helical fragment in different solvents populates an ensemble of states that is more complex than that of the hairpin, and thus the associated experimental observables (circular‐dichroism spectra, secondary chemical shifts, m values), that we back‐calculated from the simulations and compared with the actual data, are more difficult to interpret. We observed that in the case of both peptides, urea binds tightly to their backbone, while guanidine exerts its denaturing effect in a more subtle way, strongly affecting the electrostatic properties of the solution. This difference can have consequences in the way denaturation experiments are interpreted. Proteins 2017; 85:753–763. © 2016 Wiley Periodicals, Inc.     

Ab initio molecular metadynamics simulation for S-nitrosylation by nitric oxide: S-nitroxide as the key intermediate

Abstract

Snitric oxide plays important roles in protein S-nitrosylation, in which thionitroxide (RSNHO) may serve as a signal at the cysteine site. Car-Parrinello metadynamics method was employed to investigate the possible fate of thionitroxide (S-nitroxide) in S-nitrosylation, focusing on S–N decomposition that leads to HNO, NO and even thiyl radical. As a result, the lowest-energy pathway from thiol towards S-nitrosothiol via thionitroxide was predicted to be feasible in a form of RSH + 2 NO? = RSNO + HNO. This equilibrium for the chemical modification was likely controlled by surrounding environment, that is, by aqueous solution and methanol in this simulation, and probably by dynamic structure of polar residues in S-nitrosylated protein. This work implied that the general importance of the temporal and spatial transformation of allosteric effect in a predictive modelling of protein post-translational modification could be briefly attested with the artificially intelligent CPMD algorithm.     

Molecular Basis of Filtering Carbapenems by Porins from β-Lactam-resistant Clinical Strains of Escherichia coli

Integral membrane proteins known as porins are the major pathway by which hydrophilic antibiotics cross the outer membrane of Gram-negative bacteria. Single point mutations in porins can decrease the permeability of an antibiotic, either by reduction of channel size or modification of electrostatics in the channel, and thereby confer clinical resistance. Here, we investigate four mutant OmpC proteins from four different clinical isolates of Escherichia coli obtained sequentially from a single patient during a course of antimicrobial chemotherapy. OmpC porin from the first isolate (OmpC20) undergoes three consecutive and additive substitutions giving rise to OmpC26, OmpC28, and finally OmpC33. The permeability of two zwitterionic carbapenems, imipenem and meropenem, measured using liposome permeation assays and single channel electrophysiology differs significantly between OmpC20 and OmpC33. Molecular dynamic simulations show that the antibiotics must pass through the constriction zone of porins with a specific orientation, where the antibiotic dipole is aligned along the electric field inside the porin. We identify that changes in the vector of the electric field in the mutated porin, OmpC33, create an additional barrier by “trapping” the antibiotic in an unfavorable orientation in the constriction zone that suffers steric hindrance for the reorientation needed for its onward translocation. Identification and understanding the underlying molecular details of such a barrier to translocation will aid in the design of new antibiotics with improved permeation properties in Gram-negative bacteria.