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

XANES study of iron displacement in the haem of myoglobin

The XANES (X‐ray absorption near edge structure) spectra of deoxy human adult haemoglobin (HbA) and myoglobin (Mb) have been measured at the wiggler beam line of the Frascati synchrotron radiation facility. The XANES are interpreted by the multiple scattering cluster theory. The variations in the XANES between HbA and Mb are assigned to changes in the Fe‐porphyrin geometry

Electrochemical probing of selective haemoglobin binding in hydrogel-based molecularly imprinted polymers

An electrochemical method has been developed for the probing of hydrogel-based molecularly imprinted polymers (HydroMIPs) on the surface of a glassy carbon electrode. HydroMIPs designed for bovine haemoglobin selectivity were electrochemically characterised and their rebinding properties were monitored using cyclic voltammetry. The electrochemical reduction of bovine oxyhaemoglobin (BHb) in solution was observed to occur at ?0.460 V vs (Ag/AgCl) in 150 mM phosphate buffer solution (PBS). When the protein was selectively bound to the MIP, the electrochemical reduction of oxyhaemoglobin could be observed at a similar peak potential of ?0.480 V vs (Ag/AgCl). When analysing the non-imprinted control polymer (NIP) interfaced at the electrode, which contained no protein, the peak reduction potential corresponded to that observed for dissolved oxygen in solution (?0.65 V vs (Ag/AgCl)). MIP and NIP (in the absence of protein) were interfaced at the electrode and protein allowed to diffuse through the polymers from the bulk solution end to the electrode. It was observed that whereas NIP exhibited a protein response within 10 min of protein exposure, up to 45 min of exposure time was required in the case of the MIP before a protein response could be obtained. Our results suggest that due to the selective nature of the MIP, BHb arrival at the electrode via diffusion is delayed by the MIP due to attractive selective interactions with exposed cavities, but not the NIP which is devoid of selective cavities

Photochemical Pump and NMR Probe to monitor the formation and kinetics of hyperpolarized metal dihydrides

On reaction of IrI(CO)(PPh 3) 21with para-hydrogen(p-H 2),Ir(H) 2I(CO)(PPh 3) 22 is formed which exhibits strongly enhanced 1H NMR signals for its hydride resonances. Complex 2 also shows similar enhancement of its NMR spectra when it is irradiated under p-H 2. We report the use of this photochemical reactivity to measure the kinetics of H 2 addition by laser-synchronized reactions in conjunction with NMR. The single laser pulse promotes the reductive elimination of H 2 from Ir(H) 2I(CO)(PPh 3) 22 in C 6D 6 solution to form the 16-electron precursor 1, back reaction with p-H 2 then reforms 2 in a well-defined nuclear spin-state. The build up of this product can be followed by incrementing a precisely controlled delay (τ), in millisecond steps, between the laser and the NMR pulse. The resulting signal vs. time profile shows a dependence on p-H 2 pressure. The plot of k obs against p-H 2 pressure is linear and yields the second order rate constant, k 2, for H 2 addition to 1 of (3.26 ± 0.42) × 10 2 M −1 s −1. Validation was achieved by transient-UV-vis absorption spectroscopy which gives k 2 of (3.06 ± 0.40) × 10 2 M −1 s −1. Furthermore, irradiation of a C 6D 6 solution of 2 with multiple laser shots, in conjunction with p-H 2 derived hyperpolarization, allows the detection and characterisation of two minor reaction products, 2a and 3, which are produced in such low yields that they are not detected without hyperpolarization. Complex 2a is a configurational isomer of 2, while 3 is formed by substitution of CO by PPh

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

Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation.

The extracellular hemoglobin of Ascaris has an extremely high oxygen affinity (P50 = 0.004 mmHg). It consists of eight identical subunits of molecular weight 40,600. Their sequence, determined by protein chemistry, shows two tandemly linked globin-like sequences and an 18-residue C-terminal extension. Two N-linked glycosylation sites contain equal ratios of mannose/glucosamine/fucose of 3:2:1. Electron micrographs suggest that the eight subunits form a polyhedron of point symmetry D4, or 42. The C-terminal extension contains a repeat of the sequence Glu-Glu-His-Lys, which would form a pattern of alternate glutamate and histidine side chains on one side and of glutamate and lysine side chains on the other side of a beta strand. We propose that this represents a polar zipper sequence and that the C-terminal extensions are joined in an eight-stranded beta barrel at the center of the molecule, with histidine and glutamate side chains inside and lysine and glutamate side chains outside the barrel compensating each other's charges. The amino acid sequence of Ascaris hemoglobin fails to explain its high oxygen affinity

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

Structural biology and phylogenetic estimation

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62633/1/388527a0.pd

Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves a community of users with diverse backgrounds and interests. In addition to processing, archiving and distributing structural data, it also develops educational resources and materials to enable people to utilize PDB data and to further a structural view of biology