Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations

Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

<p>Abstract</p> <p>Background</p> <p>Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions.</p> <p>Results</p> <p>Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA) or in combination with α-helix (BRCT repeats) or β-sheet (WW domain) fail to differentiate pThr/pSer.</p> <p>Conclusions</p> <p>Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors.</p

Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes

AbstractAccurate free-energy calculations provide mechanistic insights into molecular recognition and conformational equilibrium. In this work, we performed free-energy calculations to study the thermodynamic properties of different states of molecular systems in their equilibrium basin, and obtained accurate absolute binding free-energy calculations for protein-ligand binding using a newly developed M2 algorithm. We used a range of Asp-Phe-Gly (DFG)-in/out p38α mitogen-activated protein kinase inhibitors as our test cases. We also focused on the flexible DFG motif, which is closely connected to kinase activation and inhibitor binding. Our calculations explain the coexistence of DFG-in and DFG-out states of the loop and reveal different components (e.g., configurational entropy and enthalpy) that stabilize the apo p38α conformations. To study novel ligand-binding modes and the key driving forces behind them, we computed the absolute binding free energies of 30 p38α inhibitors, including analogs with unavailable experimental structures. The calculations revealed multiple stable, complex conformations and changes in p38α and inhibitor conformations, as well as balance in several energetic terms and configurational entropy loss. The results provide relevant physics that can aid in designing inhibitors and understanding protein conformational equilibrium. Our approach is fast for use with proteins that contain flexible regions for structure-based drug design

Experimental Studies of Low-field Landau Quantization in Two-dimensional Electron Systems in GaAs/AlGaAs Heterostructures

By applying a magnetic field perpendicular to GaAs/AlGaAs two-dimensional electron systems, we study the low-field Landau quantization when the thermal damping is reduced with decreasing the temperature. Magneto-oscillations following Shubnikov-de Haas (SdH) formula are observed even when their amplitudes are so large that the deviation to such a formula is expected. Our experimental results show the importance of the positive magneto-resistance to the extension of SdH formula under the damping induced by the disorder.Comment: 9 pages, 3 figure

Fluctuations in Gene Regulatory Networks as Gaussian Colored Noise

The study of fluctuations in gene regulatory networks is extended to the case of Gaussian colored noise. Firstly, the solution of the corresponding Langevin equation with colored noise is expressed in terms of an Ito integral. Then, two important lemmas concerning the variance of an Ito integral and the covariance of two Ito integrals are shown. Based on the lemmas, we give the general formulae for the variances and covariance of molecular concentrations for a regulatory network near a stable equilibrium explicitly. Two examples, the gene auto-regulatory network and the toggle switch, are presented in details. In general, it is found that the finite correlation time of noise reduces the fluctuations and enhances the correlation between the fluctuations of the molecular components.Comment: 10 pages, 4 figure

Genetic Polymorphisms of the Glycine N-Methyltransferase and Prostate Cancer Risk in the Health Professionals Follow-Up Study

Purpose Glycine N-methyltransferase (GNMT) affects genetic stability by regulating the ratio of S-adenosylmethionine to S-adenosylhomocysteine, by binding to folate, and by interacting with environmental carcinogens. In Taiwanese men, GNMT was found to be a tumor susceptibility gene for prostate cancer. However, the association of GNMT with prostate cancer risk in other ethnicities has not been studied. It was recently reported that sarcosine, which is regulated by GNMT, increased markedly in metastatic prostate cancer. We hereby explored the association of GNMT polymorphisms with prostate cancer risk in individuals of European descent from the Health Professionals Follow-up Study (HPFS). Methods: A total of 661 incident prostate cancer cases and 656 controls were identified from HPFS. The GNMT short tandem repeat polymorphism 1 (STRP1), 4-bp insertion/deletion polymorphisms (INS/DEL) and the single nucleotide polymorphism rs10948059 were genotyped to test for their association with prostate cancer risk. Results: The rs10948059 T/T genotype was associated with a 1.62-fold increase in prostate cancer risk (95% confidence interval (CI): 1.18, 2.22) when compared with the C/C genotype. The STRP1 ≥16GAs/≥16GAs genotype was associated with decreased risk of prostate cancer when compared with the <16GAs/<16GAs genotype (odds ratio (OR) = 0.68; 95% CI: 0.46, 1.01). INS/DEL was not associated with prostate cancer risk. Haplotypes containing the rs10948059 T allele were significantly associated with increased prostate cancer risk. Conclusion: In men of European descent, the GNMT rs10948059 and STRP1 were associated with prostate cancer risk. Compared to the study conducted in Taiwanese men, the susceptibility GNMT alleles for prostate cancer had a reverse relationship. This study highlights the differences in allelic frequencies and prostate cancer susceptibility in different ethnicities

Type-II Topological Dirac Semimetals: Theory and Materials Prediction (VAl3 family)

The discoveries of Dirac and Weyl semimetal states in spin-orbit compounds led to the realizations of elementary particle analogs in table-top experiments. In this paper, we propose the concept of a three-dimensional type-II Dirac fermion and identify a new topological semimetal state in the large family of transition-metal icosagenides, MA3 (M=V, Nb, Ta; A=Al, Ga, In). We show that the VAl3 family features a pair of strongly Lorentz-violating type-II Dirac nodes and that each Dirac node consists of four type-II Weyl nodes with chiral charge +/-1 via symmetry breaking. Furthermore, we predict the Landau level spectrum arising from the type-II Dirac fermions in VAl3 that is distinct from that of known Dirac semimetals. We also show a topological phase transition from a type-II Dirac semimetal to a quadratic Weyl semimetal or a topological crystalline insulator via crystalline distortions. The new type-II Dirac fermions, their novel magneto-transport response, the topological tunability and the large number of compounds make VAl3 an exciting platform to explore the wide-ranging topological phenomena associated with Lorentz-violating Dirac fermions in electrical and optical transport, spectroscopic and device-based experiments.Comment: 28 pages, 7 Figure

New fermions on the line in topological symmorphic metals

Topological metals and semimetals (TMs) have recently drawn significant interest. These materials give rise to condensed matter realizations of many important concepts in high-energy physics, leading to wide-ranging protected properties in transport and spectroscopic experiments. The most studied TMs, i.e., Weyl and Dirac semimetals, feature quasiparticles that are direct analogues of the textbook elementary particles. Moreover, the TMs known so far can be characterized based on the dimensionality of the band crossing. While Weyl and Dirac semimetals feature zero-dimensional points, the band crossing of nodal-line semimetals forms a one-dimensional closed loop. In this paper, we identify a TM which breaks the above paradigms. Firstly, the TM features triply-degenerate band crossing in a symmorphic lattice, hence realizing emergent fermionic quasiparticles not present in quantum field theory. Secondly, the band crossing is neither 0D nor 1D. Instead, it consists of two isolated triply-degenerate nodes interconnected by multi-segments of lines with two-fold degeneracy. We present materials candidates. We further show that triplydegenerate band crossings in symmorphic crystals give rise to a Landau level spectrum distinct from the known TMs, suggesting novel magneto-transport responses. Our results open the door for realizing new topological phenomena and fermions including transport anomalies and spectroscopic responses in metallic crystals with nontrivial topology beyond the Weyl/Dirac paradigm.Comment: 24 pages, 4 figures, and 1 tabl

Ligand Binding Pathways and Conformational Transitions of the HIV Protease

It is important to determine the binding pathways and mechanisms of ligand molecules to target proteins to effectively design therapeutic drugs. Molecular dynamics (MD) is a promising computational tool that allows us to simulate protein–drug binding at an atomistic level. However, the gap between the time scales of current simulations and those of many drug binding processes has limited the usage of conventional MD, which has been reflected in studies of the HIV protease. Here, we have applied a robust enhanced simulation method, Gaussian accelerated molecular dynamics (GaMD), to sample binding pathways of the XK263 ligand and associated protein conformational changes in the HIV protease. During two of 10 independent GaMD simulations performed over 500–2500 ns, the ligand was observed to successfully bind to the protein active site. Although GaMD-derived free energy profiles were not fully converged because of insufficient sampling of the complex system, the simulations still allowed us to identify relatively low-energy intermediate conformational states during binding of the ligand to the HIV protease. Relative to the X-ray crystal structure, the XK263 ligand reached a minimum root-mean-square deviation (RMSD) of 2.26 Å during 2.5 μs of GaMD simulation. In comparison, the ligand RMSD reached a minimum of only ~5.73 Å during an earlier 14 μs conventional MD simulation. This work highlights the enhanced sampling power of the GaMD approach and demonstrates its wide applicability to studies of drug–receptor interactions for the HIV protease and by extension many other target proteins