Computational insights into substrate binding and catalytic mechanism of the glutaminase domain of glucosamine-6-phosphate synthase (GlmS)

Glucosamine-6-phosphate synthase (GlmS) is a key enzyme in the biosynthesis of hexosamine across a variety of species including Escherichia coli, fungi, and humans. In particular, its glutaminase domain catalyzes the conversion of glutamine to glutamic acid with the release of ammonia. A catalytically important cysteinyl (Cys1) has been suggested to act as the mechanistic nucleophile after being activated by the N-terminal amine of the glutaminase domain (i.e., its own α-amine). Using molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computational methods, we have investigated the active site of the glutaminase domain, the protonation state of its N-terminal amine, substrate binding, and catalytic mechanism. In addition, the potential for an active site histidyl (His71) to alternatively act as the required base was examined. The N-terminal amine is concluded to have a reduced pKa due to being buried within the enzyme and the nearby presence of a protonated arginyl residue. Previous suggestions that this was due in part to hydrogen bonding with the hydroxyl of Thr606 is not supported; such an interaction is not consistent, and accounts for only 4% of the total duration of the MD simulation. The most feasible enzymatic pathway is found to involve a neutral N-terminal Cys1 α-amine acting as a base and directly deprotonating (i.e., without the involvement of a water, the Cys1SH thiol). The tetrahedral oxyanion intermediate formed during the mechanism is stabilized by a water and two enzyme residues: Asn98 and Gly99. Furthermore, the overall rate-limiting step of the mechanism is the nucleophilic attack of a water on the thioester cross-linked intermediate with a barrier of 74.4 kJ mol−1. An alternate mechanism in which His71 acts as the nucleophile-activating base, and which requires the Cys1 α-amine to be protonated, is calculated to be enzymatically feasible but to have a much higher overall rate-limiting barrier of 93.7 kJ mol−1

Eclipses During the 2010 Eruption of the Recurrent Nova U Scorpii

The eruption of the recurrent nova U Scorpii on 28 January 2010 is now the all-time best observed nova event. We report 36,776 magnitudes throughout its 67 day eruption, for an average of one measure every 2.6 minutes. This unique and unprecedented coverage is the first time that a nova has any substantial amount of fast photometry. With this, two new phenomena have been discovered: the fast flares in the early light curve seen from days 9-15 (which have no proposed explanation) and the optical dips seen out of eclipse from days 41-61 (likely caused by raised rims of the accretion disk occulting the bright inner regions of the disk as seen over specific orbital phases). The expanding shell and wind cleared enough from days 12-15 so that the inner binary system became visible, resulting in the sudden onset of eclipses and the turn-on of the supersoft X-ray source. On day 15, a strong asymmetry in the out-of-eclipse light points to the existence of the accretion stream. The normal optical flickering restarts on day 24.5. For days 15-26, eclipse mapping shows that the optical source is spherically symmetric with a radius of 4.1 R_sun. For days 26-41, the optical light is coming from a rim-bright disk of radius 3.4 R_sun. For days 41-67, the optical source is a center-bright disk of radius 2.2 R_sun. Throughout the eruption, the colors remain essentially constant. We present 12 eclipse times during eruption plus five just after the eruption.Comment: ApJ in press. 60 pages, 17 figure

Impact of deamidation on the structure and function of anti-apoptotic Bcl-xL.

Bcl-xL is an anti-apoptotic mitochondrial trans-membrane protein, known to play a crucial role in the survival of tumor cells. The deamidation of Bcl-xL is a pivotal switch that regulates its biological function. The potential impact of deamidation on the structure and dynamics of Bcl-xL is directly linked to the intrinsically disordered region (IDR), which is the main site for post-translational modifications (PTMs). In this study, we explored deamidation-induced conformational changes in Bcl- xL to gain insight into its loss of function by performing microsecond-long molecular dynamics (MD) simulations. MD simulation outcomes showed that the IDR motion and interaction patterns have changed notably upon deamidation. Principal component analysis (PCA) demonstrates significant differences between wild type and deamidated Bcl-xL and suggests that deamidation affects the structure and dynamics of Bcl-xL. Differences in contact patterns and essential dynamics in the binding groove (BG) are clear indications of deamidation-induced allosteric affects

Semi-Empirical Born–Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package

International audienceSemi-empirical quantum methods from the neglect of differential diatomic overlap (NDDO) family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By combining them with linear scaling methods like the divide & conquer (D&C) method, it is possible to quickly evaluate the energy of systems containing hundreds to thousands of atoms. We here present our implementation in the Amber biomolecular package of a SEBOMD module that provides a way to run semi-empirical Born−Oppenheimer molecular dynamics. At each step of a SEBOMD, a fully converged self-consistent field (SCF) calculation is performed to obtain the semiempirical quantum potential energy of a molecular system encaged or not in periodic boundary conditions. We describe the implementation and the features of our SEBOMD implementation. We show the requirements to conserve the total energy in NVE simulations, and how to accelerate SCF convergence through density matrix extrapolation. Specific ways of handling periodic boundary conditions using mechanical embedding or electrostatic embedding through a tailored quantum Ewald summation is developed. The parallel performance of SEBOMD simulations using the D&C scheme are presented for liquid water systems of various sizes, and a comparison between the traditional full diagonalization scheme and the D&C approach for the reproduction of the structure of liquid water illustrates the potentiality of SEBOMD to simulate molecular systems containing several hundreds of atoms for hundreds of picoseconds with a quantum mechanical potential in a reasonable amount of CPU time

Impact of Deamidation on the Structure and Function of Antiapoptotic Bcl-x L

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SemiEmpirical Born-Oppenheimer Molecular Dynamics (SEBOMD) Within the Amber Biomolecular Package

Semiempirical quantum methods from the Neglect of Differential Diatomic Overlap (NDDO) family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By combining them with linear scaling methods like the Divide & Conquer (D&C) method, it is possible to quickly evaluate the energy of systems containing hundreds to thousands of atoms. We here present our implementation in the Amber biomolecular package of a SEBOMD module that provides a way to run SemiEmpirical Born-Oppenheimer Molecular Dynamics. At each step of a SEBOMD molecular dynamics, a fully converged SCF calculation is performed to obtain the semiempirical quantum potential energy of a molecular system encaged or not in periodic boundary conditions. We describe the implementation and the features of our SEBOMD implementation. We show the equirements to conserve the total energy in NVE simulations, and how to accelerate SCF convergence through density matrix extrapolation. Specific ways of handling periodic boundary conditions using mechanical embedding or electrostatic embedding through a tailored quantum Ewald summation is developed. The parallel performance of SEBOMD simulations using the D&C scheme are presented for liquid water systems of various sizes, and a comparison between the traditional full diagonalization scheme and the D&C approach for the reproduction of the structure of liquid water illustrates the potentiality of SEBOMD to simulate molecular systems containing several hundreds of atoms for hundreds of picoseconds with a quantum mechanical potential in a reasonable amount of CPU time.</div

Why Does Asn71 Deamidate Faster Than Asn15 in the Enzyme Triosephosphate Isomerase? Answers from Microsecond Molecular Dynamics Simulation and QM/MM Free Energy Calculations

Deamidation is the uncatalyzed process by which asparagine or glutamine can be transformed into aspartic acid or glutamic acid, respectively. In its active homodimeric form, mammalian triosephosphate isomerase (TPI) contains two deamidation sites per monomer. Experimental evidence shows that the primary deamidation site (Asn71-Gly72) deamidates faster than the secondary deamidation site (Asn15-Gly16). To evaluate the factors controlling the rates of these two deamidation sites in TPI, we have performed graphics processing unit-enabled microsecond long molecular dynamics simulations of rabbit TPI. The kinetics of asparagine dipeptide and two deamidation sites in mammalian TPI are also investigated using quantum mechanical/molecular mechanical tools with the umbrella sampling technique. Analysis of the simulations has been performed using independent global and local descriptors that can influence the deamidation rates: desolvation effects, backbone acidity, and side chain conformations. Our findings show that all the descriptors add up to favor the primary deamidation site over the secondary one in mammalian TPI: Asn71 deamidates faster because it is more solvent accessible, the adjacent glycine NH backbone acidity is enhanced, and the Asn side chain has a preferential near attack conformation. The crucial impact of the backbone amide acidity of the adjacent glycine on the deamidation rate is shown by kinetic analysis. Our findings also shed light on the effect of high-order structure on deamidation: the deamidation in a small peptide is favored first because of the higher reactivity of the asparagine residue and then because of the stronger stability of the tetrahedral intermediate

What is the effective dielectric constant in a β-cyclodextrin cavity? Insights from Molecular Dynamics simulations and QM/MM calculations

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