Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\alpha}1{\beta}2 and {\alpha}2{\beta}1 interface.Comment: Reprinted (adapted) with permission from J. Phys. Chem. B DOI:10.1021/jp3022908. Copyright (2012) American Chemical Societ

Deer mouse hemoglobin exhibits a lowered oxygen affinity owing to mobility of the E helix

The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was expressed in Escherichia coli and was purified by ion-exchange chromatography. Recombinant hemoglobin was crystallized by the hangingdrop vapor-diffusion method using polyethylene glycol as a precipitant. The obtained orthorhombic crystal contained two subunits in the asymmetric unit. The refined structure was interpreted as the aquo-met form. Structural comparisons were performed among hemoglobins from deer mouse, house mouse and human. In contrast to human hemoglobin, deer mouse hemoglobin lacks the hydrogen bond between α1Trp14 in the A helix and α1Thr67 in the E helix owing to the Thr67Ala substitution. In addition, deer mouse hemoglobin has a unique hydrogen bond at the α1β1 interface between residues α1Cys34 and β1Ser128

Local Simulation Algorithms for Coulomb Interaction

Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow equilibration using a local Hamiltonian. The method introduces an auxiliary field with constrained dynamics so that the equilibrium distribution is determined by the Coulomb interaction. We demonstrate the efficiency of the method by simulating a simple, charged lattice gas.Comment: Last figure changed to improve demonstration of numerical efficienc

Improving the photocatalytic reduction of CO2 to CO through immobilisation of a molecular Re catalyst on TiO2.

The photocatalytic activity of phosphonated Re complexes, [Re(2,2'-bipyridine-4,4'-bisphosphonic acid) (CO)3(L)] (ReP; L = 3-picoline or bromide) immobilised on TiO2 nanoparticles is reported. The heterogenised Re catalyst on the semiconductor, ReP-TiO2 hybrid, displays an improvement in CO2 reduction photocatalysis. A high turnover number (TON) of 48 molCO molRe(-1) is observed in DMF with the electron donor triethanolamine at λ>420 nm. ReP-TiO2 compares favourably to previously reported homogeneous systems and is the highest TON reported to date for a CO2-reducing Re photocatalyst under visible light irradiation. Photocatalytic CO2 reduction is even observed with ReP-TiO2 at wavelengths of λ>495 nm. Infrared and X-ray photoelectron spectroscopies confirm that an intact ReP catalyst is present on the TiO2 surface before and during catalysis. Transient absorption spectroscopy suggests that the high activity upon heterogenisation is due to an increase in the lifetime of the immobilised anionic Re intermediate (t50% >1 s for ReP-TiO2 compared with t50% = 60 ms for ReP in solution) and immobilisation might also reduce the formation of inactive Re dimers. This study demonstrates that the activity of a homogeneous photocatalyst can be improved through immobilisation on a metal oxide surface by favourably modifying its photochemical kinetics.Financial support from the EPSRC (EP/H00338X/2 to E.R.; studentship and Doctoral Prize to C.D.W.; DTP scholarship to E.P.), the Christian Doppler Research Association (Austrian Federal Ministry of Science, Research and Economy and the 28 National Foundation for Research, Technology and Development) and the OMV Group (to E.R.), the ERC (project Intersolar to J.D.) and the European Commission Marie Curie CIG (PCIG10-GA-2011-303650 to A.R.) is gratefully acknowledged.This is the final published version. It first appeared in Chemistry - a European Journal, 2015, 21, 3746 – 3754, DOI: 10.1002/chem.20140504

Notes on bordered Floer homology

This is a survey of bordered Heegaard Floer homology, an extension of the Heegaard Floer invariant HF-hat to 3-manifolds with boundary. Emphasis is placed on how bordered Heegaard Floer homology can be used for computations.Comment: 73 pages, 29 figures. Based on lectures at the Contact and Symplectic Topology Summer School in Budapest, July 2012. v2: Fixed many small typo

Kinetics of stochastically-gated diffusion-limited reactions and geometry of random walk trajectories

In this paper we study the kinetics of diffusion-limited, pseudo-first-order A + B -> B reactions in situations in which the particles' intrinsic reactivities vary randomly in time. That is, we suppose that the particles are bearing "gates" which interchange randomly and independently of each other between two states - an active state, when the reaction may take place, and a blocked state, when the reaction is completly inhibited. We consider four different models, such that the A particle can be either mobile or immobile, gated or ungated, as well as ungated or gated B particles can be fixed at random positions or move randomly. All models are formulated on a $d$-dimensional regular lattice and we suppose that the mobile species perform independent, homogeneous, discrete-time lattice random walks. The model involving a single, immobile, ungated target A and a concentration of mobile, gated B particles is solved exactly. For the remaining three models we determine exactly, in form of rigorous lower and upper bounds, the large-N asymptotical behavior of the A particle survival probability. We also realize that for all four models studied here such a probalibity can be interpreted as the moment generating function of some functionals of random walk trajectories, such as, e.g., the number of self-intersections, the number of sites visited exactly a given number of times, "residence time" on a random array of lattice sites and etc. Our results thus apply to the asymptotical behavior of the corresponding generating functions which has not been known as yet.Comment: Latex, 45 pages, 5 ps-figures, submitted to PR

Academic freedom: in justification of a universal ideal

This paper examines the justification for, and benefits of, academic freedom to academics, students, universities and the world at large. The paper surveys the development of the concept of academic freedom within Europe, more especially the impact of the reforms at the University of Berlin instigated by Wilhelm von Humboldt. Following from this, the paper examines the reasons why the various facets of academic freedom are important and why the principle should continue to be supported

Structural Properties of Polyglutamine Aggregates Investigated via Molecular Dynamics Simulations

Polyglutamine (polyQ) beta-stranded aggregates constitute the hallmark of Huntington disease. The disease is fully penetrant when Q residues are more than 36-40 ("disease threshold"). Here, based on a molecular dynamics study on polyQ helical structures of different shapes and oligomeric states, we suggest that the stability of the aggregates increases with the number of monomers, while it is rather insensitive to the number of Qs in each monomer. However, the stability of the single monomer does depend on the number of side-chain intramolecular H-bonds, and therefore oil the number of Qs. If such number is lower than that of the disease threshold, the beta-stranded monomers are unstable and hence may aggregate with lower probability, consistently with experimental findings. Our results provide a possible interpretation of the apparent polyQ length dependent-toxicity, and they do not support the so-called "structural threshold hypothesis", which supposes a transition from random coil to a beta-sheet structure only above the disease threshold