2005 - Abstracts
1. Bergeon, N., R. Trivedi, B. Billia, B. Echebarria, A. Karma, S. Liu, C. Weiss and N. Mangelinck (2005). "Necessity of investigating microstructure formation during directional solidification of transparent alloys in 3D." Low Gravity Phenomena and Condensed Matter Experiments in Space 36(1): 80-85.
The properties of structural materials are to a large extent determined by the solid microstructure so that the understanding of the fundamental physics of microstructure formation is critical in the engineering of materials. Also, microstructure selection occurs during the dynamical growth process so that in situ observation of spatio-temporal evolution of the solid-liquid interface shape is necessary. Under terrestrial conditions convection effects dominate in bulk samples, which prevents precise characterization of microstructure selection. Diffusion-controlled experiments in thin samples give microstructures that are neither 2D nor 3D. Rigorous theoretical models using the phase-field method have shown that the fundamental physics of pattern selection in 2D and 3D is significantly different. A benchmark experimental study in bulk samples is thus required under low gravity conditions. In the frame of the joint work of DSIP and MISOL3D projects, respectively, selected by NASA and CNES, microgravity experiments in a model transparent system are planned on ISS using the directional solidification insert (DSI) in the DECLIC facility. The critical aspects of hardware design, the key fundamental issues identified through 1g-experiments, the proposed study on ISS, and the results of rigorous theoretical modeling are presented. (c) 2005 COSPAR. Published by Elsevier Ltd. All rights reserved.
2. Champion, P. M. (2005). "Chemistry - Following the flow of energy in biomolecules." Science 310(5750): 980-982.
3. Fenton, F. H., E. M. Cherry, A. Karma and W. J. Rappel (2005). "Modeling wave propagation in realistic heart geometries using the phase-field method." Chaos 15(1): 013502.
We present a novel algorithm for modeling electrical wave propagation in anatomical models of the heart. The algorithm uses a phase-field approach that represents the boundaries between the heart muscle and the surrounding medium as a spatially diffuse interface of finite thickness. The chief advantage of this method is to automatically handle the boundary conditions of the voltage in complex geometries without the need to track the location of these boundaries explicitly. The algorithm is shown to converge accurately in nontrivial test geometries with no-flux (zero normal current) boundary conditions as the width of the diffuse interface becomes small compared to the width of the cardiac action potential wavefront. Moreover, the method is illustrated for anatomically realistic models of isolated rabbit and canine ventricles as well as human atria. (C) 2005 American Institute of Physics.
4. Hakim, V. and A. Karma (2005). "Crack path prediction in anisotropic brittle materials." Physical Review Letters 95(23): 235501.
A force balance condition to predict quasistatic crack paths in anisotropic brittle materials is derived from an analysis of diffuse interface continuum models that describe both short-scale failure and macroscopic linear elasticity. The path is uniquely determined by the directional anisotropy of the fracture energy, independent of details of the failure process. The derivation exploits the gradient dynamics and translation symmetry properties of this class of models to define a generalized energy-momentum tensor whose integral around an arbitrary closed path enclosing the crack tip yields all forces acting on this tip, including Eshelby's configurational forces, cohesive forces, and dissipative forces. Numerical simulations are in very good agreement with analytic predictions.
5. Lonascu, D., F. Gruia, X. Ye, A. C. Yu, F. Rosca, C. Beck, A. Demidov, J. S. Olson and P. M. Champion (2005). "Temperature-dependent studies of NO recombination to heme and heme proteins." Journal of the American Chemical Society 127(48): 16921-16934.
The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (similar to 10 ps) recombination phase is found to be zero and a slower geminate phase (similar to 200 ps) reveals a small enthalpic barrier (similar to 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (similar to 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (onthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.
6. Karma, A. and A. E. Lobkovsky (2005). "Low-temperature dynamics of kinks on Ising interfaces." Physical Review E 71(3): 036114.
The anisotropic motion of an interface driven by its intrinsic curvature or by an external field is investigated in the context of the kinetic Ising model in both two and three dimensions. We derive in two dimensions (2D) a continuum evolution equation for the density of kinks by a time-dependent and nonlocal mapping to the asymmetric exclusion process. Whereas kinks execute random walks biased by the external field and pile up vertically on the physical 2D lattice, they execute hard-core biased random walks on a transformed 1D lattice. Their density obeys a nonlinear diffusion equation which can be transformed into the standard expression for the interface velocity, v=M[(gamma+gamma')kappa+H], where M, gamma+gamma', and kappa are the interface mobility, stiffness, and curvature, respectively. In 3D, we obtain the velocity of a curved interface near the < 100 > orientation from an analysis of the self-similar evolution of 2D shrinking terraces. We show that this velocity is consistent with the one predicted from the 3D tensorial generalization of the law for anisotropic curvature-driven motion. In this generalization, both the interface stiffness tensor and the curvature tensor are singular at the < 100 > orientation. However, their product, which determines the interface velocity, is smooth. In addition, we illustrate how this kink-based kinetic description provides a useful framework for studying more complex situations by modeling the effect of immobile dilute impurities.
7. Leu, B. M., M. Z. Zgierski, G. R. A. Wyllie, M. K. Ellison, W. R. Scheidt, W. Sturhahn, E. E. Alp, S. M. Durbin and J. T. Sage (2005). "Vibrational dynamics of biological molecules: Multi-quantum contributions." Journal of Physics and Chemistry of Solids 66(12): 2250-2256.
High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of Fe-57 vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available. (c) 2005 Elsevier Ltd. All rights reserved.
8. Martin, S. L., M. Cruceanu, D. Branciforte, P. W. I. Li, S. C. Kwok, R. S. Hodges and M. C. Williams (2005). "LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein." Journal of Molecular Biology 348(3): 549-561.
LINE-1 is a highly successful, non-LTR retrotransposon that has played a leading role in shaping mammalian genomes. These elements move autonomously through an RNA intermediate using target-primed reverse transcription (TPRT). L1 encodes two essential polypeptides for retro-transposition, the products of its two open reading frames, ORF1 and ORF2. The exact function of the ORF1 protein (ORF1p) in L1 retrotransposition is unknown, although it is an RNA-binding protein that can act as a nucleic acid chaperone. Here, we investigate the requirements for these two activities in L1 retrotransposition by examining the consequences of mutating two adjacent and highly conserved arginine residues in the ORF1p from mouse L1. Substitution of both arginine residues with alanine strongly reduces the affinity of the protein for single-stranded nucleic acid whereas substitution of one or both with lysine has only minimal effects on this feature. Rather, the lysine substitutions alter the delicate balance between the ORF1 protein's melting and reannealing activities, thereby reducing its nucleic acid chaperone activity. These findings establish the importance of the nucleic acid chaperone activity of ORF1p to successful L1 retrotransposition, and provide insight into the essential properties of nucleic acid chaperones. (c) 2005 Elsevier Ltd. All rights reserved.
9. McCauley, M., P. R. Hardwidge, L. J. Maher and M. C. Williams (2005). "Dual binding modes for an HMG domain from human HMGB2 on DNA." Biophysical Journal 89(1): 353-364.
High mobility group B ( HMGB) proteins contain two HMG box domains known to bind without sequence specificity into the DNA minor groove, slightly intercalating between basepairs and producing a strong bend in the DNA backbone. We use optical tweezers to measure the forces required to stretch single DNA molecules. Parameters describing DNA flexibility, including contour length and persistence length, are revealed. In the presence of nanomolar concentrations of isolated HMG box A from HMGB2, DNA shows a decrease in its persistence length, where the protein induces an average DNA bend angle of 114 +/- 21 degrees for 50 mM Na+, and 87 +/- 9 degrees for 100 mM Na+. The DNA contour length increases from 0.341 +/- 0.003 to 0.397 +/- 0.012 nm per basepair, independent of salt concentration. In 50 mM Na+, the protein does not unbind even at high DNA extension, whereas in 100 mM Na+, the protein appears to unbind only below concentrations of 2 nM. These observations support a flexible hinge model for noncooperative HMG binding at low protein concentrations. However, at higher protein concentrations, a cooperative. lament mode is observed instead of the hinge binding. This mode may be uniquely characterized by this high-force optical tweezers experiment.
10. Pant, K., R. L. Karpel, I. Rouzina and M. C. Williams (2005). "Salt dependent binding of T4 gene 32 protein to single and double-stranded DNA: Single molecule force spectroscopy measurements." Journal of Molecular Biology 349(2): 317-330.
Bacteriophage T4 gene 32 protein (gp32) is a well-studied representative of the large family of single-stranded DNA (ssDNA) binding proteins, which are essential for DNA replication, recombination and repair. Surprisingly, gp32 has not previously been observed to melt natural dsDNA. At the same time, *I, a truncated version of gp32 lacking its C-terminal domain (CTD), was shown to decrease the melting temperature of natural DNA by about 50 deg. C. This profound difference in the duplex destabilizing ability of gp32 and *I is especially puzzling given that the previously measured binding of both proteins to ssDNA was similar. Here, we resolve this apparent contradiction by studying the effect of gp32 and *I on the thermodynamics and kinetics of duplex DNA melting. We use a previously developed single molecule technique for measuring the non-cooperative association constants (K-ds) to double-stranded DNA to determine Kds as a function of salt concentration for gp32 and *I. We then develop a new single molecule method for measuring K, the association constant of these proteins to ssDNA. Comparing our measured binding constants to ssDNA for gp32 and *I we see that while they are very similar in high salt, they strongly diverge at [Na+] < 0.2 M. These results suggest that intact protein must undergo a conformational rearrangement involving the CTD that is in pre-equilibrium to its non-cooperative binding to both dsDNA and ssDNA. This lowers the effective concentration of protein available for binding, which in turn lowers the rate at which it can destabilize dsDNA. For the first time, we quantify the free energy of this CTD unfolding, and show it to be strongly salt dependent and associated with sodium counter-ion condensation on the CTD. (c) 2005 Published by Elsevier Ltd.
11. Rouzina, I., K. Pant, R. L. Karpel and M. C. Williams (2005). "Theory of electrostatically regulated binding of T4 gene 32 protein to single- and double-stranded DNA." Biophysical Journal 89(3): 1941-1956.
Bacteriophage T4 gene 32 protein (gp32) is a single-stranded DNA binding protein, which is essential for DNA replication, recombination, and repair. In a recent article, we described a new method using single DNA molecule stretching measurements to determine the noncooperative association constants K-ds to double-stranded DNA for gp32 and *I, a truncated form of gp32. In addition, we developed a single molecule method for measuring K-ss, the association constant of these proteins to single-stranded DNA. We found that in low salt both K-ds and K-ss have a very weak salt dependence for gp32, whereas for *I the salt dependence remains strong. In this article we propose a model that explains the salt dependence of gp32 and *I binding to single-stranded nucleic acids. The main feature of this model is the strongly salt-dependent removal of the C-terminal domain of gp32 from its nucleic acid binding site that is in pre-equilibrium to protein binding to both double-stranded and single-stranded nucleic acid. We hypothesize that unbinding of the C-terminal domain is associated with counterion condensation of sodiumions onto this part of gp32, which compensates for sodium ion release from the nucleic acid upon its binding to the protein. This results in the salt-independence of gp32 binding to DNA in low salt. The predictions of our model quantitatively describe the large body of thermodynamic and kinetic data from bulk and single molecule experiments on gp32 and *I binding to single-stranded nucleic acids.
12. Sage, J. T. (2005). "Vibrational dynamics of iron in biological molecules." Abstracts of Papers of the American Chemical Society 229: U1077-U1077.
13. Scheidt, W. R., S. M. Durbin and J. T. Sage (2005). "Nuclear resonance vibrational spectroscopy - NRVS." Journal of Inorganic Biochemistry 99(1): 60-71.
The recent, synchrotron-based vibrational technique nuclear resonance vibrational spectroscopy (NRVS) is introduced. The method can be used for a number of Mossbauer active isotopes including 57 Fe, which has yielded most of the results to date. The NRVS experiment can be thought of as Mossbauer spectroscopy with vibrational sidebands. Importantly, the NRVS experiment provides the complete set of bands corresponding to modes that involve motion of the iron atom. The method has a selectivity reminiscent of that of resonance Raman spectroscopy, but with the significant advantage that NRVS is not subject to the optical selection rules of Raman or infrared spectroscopy. Indeed, NRVS provides the ultimate limit in selectivity because only the vibrational dynamics of the probe nucleus contribute to the observed signal. All iron-ligand modes will be observed, including many that had not been previously observed. For hemes, these include in-plane iron vibrations that have not yet been reported by resonance Raman studies and the iron-imidazole stretch that has not been identified in six-coordinate porphyrins. Other modes that can be investigated include that of heme doming that is expected to be a low-frequency mode. The experimental setup at a beam line and sample requirements for iron-based derivatives are presented. Both powder and polarized single-crystal measurements can be made. The general features of data extraction and analysis are given. Data for heme and heme proteins are given. Examples of assignment of spectra for nitrosyl and carbonyl derivatives are given. These data demonstrate the importance of peripheral substituents on the vibrational spectrum of heme derivatives. Delocalization of modes appears to be common. Although this technique has only been available for a relatively short time, this early progress report indicates that NRVS has significant potential for probing the dynamics of Fe-containing molecules of biological interest. (C) 2004 Elsevier Inc. All rights reserved.
14. Shepherd, G. M. G., A. Stepanyants, I. Bureau, D. Chklovskii and K. Svoboda (2005). "Geometric and functional organization of cortical circuits." Nature Neuroscience 8(6): 782-790.
Can neuronal morphology predict functional synaptic circuits? In the rat barrel cortex, 'barrels' and 'septa' delineate an orderly matrix of cortical columns. Using quantitative laser scanning photostimulation we measured the strength of excitatory projections from layer 4 (L4) and L5A to L2/3 pyramidal cells in barrel- and septum-related columns. From morphological reconstructions of excitatory neurons we computed the geometric circuit predicted by axodendritic overlap. Within most individual projections, functional inputs were predicted by geometry and a single scale factor, the synaptic strength per potential synapse. This factor, however, varied between projections and, in one case, even within a projection, up to 20-fold. Relationships between geometric overlap and synaptic strength thus depend on the laminar and columnar locations of both the pre- and postsynaptic neurons, even for neurons of the same type. A large plasticity potential appears to be incorporated into these circuits, allowing for functional 'tuning' with fixed axonal and dendritic arbor geometry.
15. Shiferaw, Y., D. Sato and A. Karma (2005). "Coupled dynamics of voltage and calcium in paced cardiac cells." Physical Review E 71(2): 021903.
We investigate numerically and analytically the coupled dynamics of transmembrane voltage and intracellular calcium cycling in paced cardiac cells using a detailed physiological model, and its reduction to a three-dimensional discrete map. The results provide a theoretical framework to interpret various experimentally observed modes of instability ranging from electromechanically concordant and discordant alternans to quasiperiodic oscillations of voltage and calcium.
16. Sokoloff, J. B. (2005). "Theory of lubrication due to collective pinning." Physical Review E 71(5): 056107.
In collective pinning theory, the problem of two three-dimensional solids in contact is at its critical dimension. This implies that when the disordered forces acting between the two solids at the interface are relatively strong, the force of static friction should be large, but at smaller values of these forces, the system switches over to a regime of weak static friction. It is argued that this provides a mechanism for the reduction of friction in boundary lubrication. Lubricant molecules reduce static friction by smoothing the roughness of the surface, thus allowing the force pushing the surfaces together to be supported by more points of contact, which can switch the interface from the strong- to weak-static-friction regime.
17. Sokolov, I. M., R. Metzler, K. Pant and M. C. Williams (2005). "First passage time of N excluded-volume particles on a line." Physical Review E 72(4): 041102.
Motivated by recent single-molecule studies of proteins sliding on a DNA molecule, we explore the targeting dynamics of N particles ("proteins") sliding diffusively along a line ("DNA") in search of their target site (specific target sequence). At lower particle densities, one observes an expected reduction of the mean first passage time proportional to N-2, with corrections at higher concentrations. We explicitly take adsorption and desorption effects, to and from the DNA, into account. For this general case, we also consider finite-size effects when the continuum approximation based on the number density of particles breaks down. Moreover, we address the first-passage-time problem of a tagged particle diffusing among other particles.
18. Sokolov, I. M., R. Metzler, K. Pant and M. C. Williams (2005). "Target search of N sliding proteins on a DNA." Biophysical Journal 89(2): 895-902.
At low to moderate ambient salt concentrations, DNA-binding proteins bind relatively tightly to DNA, and only very rarely detach. Intersegmental transfer due to DNA-looping can be excluded by applying an external pulling force to the DNA molecule. Under such conditions, we explore the targeting dynamics of N proteins sliding diffusively along DNA in search of their specific target sequence. At lower densities of binding proteins, we find a reduction of the characteristic search time proportional to N-2, with corrections at higher concentrations. Rates for detachment and attachment of binding proteins are incorporated in the model. Our findings are in agreement with recent single molecule studies in the presence of bacteriophage T4 gene 32 protein for which the unbinding rate is much lower than the specific binding rate.
19. Stepanyants, A. and D. B. Chklovskii (2005). "Neurogeometry and potential synaptic connectivity." Trends in Neurosciences 28(7): 387-394.
The advent of high-quality 3D reconstructions of neuronal arbors has revived the hope of inferring synaptic connectivity from the geometric shapes of axons and dendrites, or 'neurogeometry'. A quantitative description of connectivity must be built on a sound theoretical framework. Here, we review recent developments in neurogeometry that can provide such a framework. We base the geometric description of connectivity on the concept of a 'potential synapse' - the close apposition between axons and dendrites necessary to form an actual synapse. In addition to describing potential synaptic connectivity in neuronal circuits, neurogeometry provides insight into basic features of functional connectivity, such as specificity and plasticity.
20. van Thor, J. J., G. Y. Georgiev, M. Towrie and J. T. Sage (2005). "Ultrafast and low barrier motions in the photoreactions of the green fluorescent protein." Journal of Biological Chemistry 280(39): 33652-33659.
Green fluorescent protein (GFP) fluoresces efficiently under blue excitation despite major electrostatic rearrangements resulting from photoionization of the chromophore and neutralization of Glu-222. A competing phototransformation process, which ionizes the chromophore and decarboxylates Glu-222, mimics the electrostatic and structural changes in the fluorescence photocycle. Structural and spectroscopic analysis of the cryogenically stabilized photoproduct at 100 K and a structurally annealed intermediate of the phototransformed protein at 170 K reveals distinct structural relaxations involving protein, chromophore, solvent, and photogenerated CO2. Strong structural changes of the 100 K photoproduct after decarboxylation appear exclusively within 15 angstrom of the chromophore and include the electrostatically driven perturbations of Gln-69, Cys-70, and water molecules in an H-bonding network connecting the chromophore. X-ray crystallography to 1.85 angstrom resolution and static and picosecond time-resolved IR spectroscopy identify structural mechanisms common to phototransformation and to the fluorescence photocycle. In particular, the appearance of a 1697 cm(-1) (+) difference band in both photocycle and phototransformation intermediates is a spectroscopic signature for the structural perturbation of Gln-69. This is taken as evidence for an electrostatically driven dynamic response that is common to both photoreaction pathways. The interactions between the chromophore and the perturbed residues and solvent are decreased or removed in the T203H single and T203H/Q69L double mutants, resulting in a strong reduction of the fluorescence quantum yield. This suggests that the electrostatic response to the transient formation of a buried charge in the wild type is important for the bright fluorescence.
21. Vladescu, I. D., M. J. McCauley, I. Rouzina and M. C. Williams (2005). "Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium." Physical Review Letters 95(15): 158102.
When a single DNA molecule is stretched beyond its normal contour length, a force-induced melting transition is observed. Ethidium binding increases the DNA contour length, decreases the elongation upon melting, and increases the DNA melting force in a manner that is consistent with the ethidium-induced changes in duplex DNA stability known from thermal melting studies. The DNA stretching curves map out a phase diagram and critical point in the force-extension-ethidium concentration space. Intercalation occurs between alternate base pairs at low forces and between every base pair at high forces.
22. Weiss, J. N., Z. L. Qu, P. S. Chen, S. F. Lin, H. S. Karagueuzian, H. Hayashi, A. Garfinkel and A. Karma (2005). "The dynamics of cardiac fibrillation." Circulation 112(8): 1232-1240.
Reentry occurs when the electrical wave propagating through the atria or ventricles breaks locally and forms a rotor (also called a scroll wave or functional reentry). If the waves propagating outward from a rotor develop additional wavebreaks ( which may form new rotors), fibrillation results. Tissue heterogeneity, exacerbated by electrical and structural remodeling from cardiac disease, has traditionally been considered the major factor promoting wavebreak and its degeneration to fibrillation. Recently, however, dynamic factors have also been recognized to play a key role. Dynamic factors refer to cellular properties of the cardiac action potential and Ca-i cycling, which dynamically generate wave instability and wavebreak, even in tissue that is initially completely homogeneous. Although the latter situation can only be created in computer simulations, its relevance to real (heterogeneous) cardiac tissue has been unequivocally demonstrated. Dynamic factors are related to membrane voltage (V-m) and Ca-i. V-m factors include electrical restitution of action potential duration and conduction velocity, short-term cardiac memory, and electrotonic currents. Ca-i factors are related to dynamic Ca-i cycling properties. They act synergistically, as well as with tissue heterogeneity, to promote wavebreak and fibrillation. As global properties, rather than local electrophysiological characteristics, dynamic factors represent an attractive target for novel therapies to prevent ventricular fibrillation.
23. Ye, X., A. C. Yu, G. Y. Georgiev, F. Gruia, D. Ionascu, W. X. Cao, J. T. Sage and P. M. Champion (2005). "CO rebinding to protoheme: Investigations of the proximal and distal contributions to the geminate rebinding barrier." Journal of the American Chemical Society 127(16): 5854-5861.
The rebinding kinetics of CO to protoheme (FePPIX) in the presence and absence of a proximal imidazole ligand reveals the magnitude of the rebinding barrier associated with proximal histidine ligation. The ligation states of the heme under different solvent conditions are also investigated using both equilibrium and transient spectroscopy. In the absence of imiclazole, a weak ligand (probably water) is bound on the proximal side of the FePPIX-CO adduct. When the heme is encapsulated in micelles of cetyltrimethylammonium bromide (CTAB), photolysis of FePPIX-CO induces a complicated set of proximal ligation changes. In contrast, the use of glycerol-water solutions leads to a simple two-state geminate kinetic response with rapid (10-100 ps) CO recombination and a geminate amplitude that can be controlled by adjusting the solvent viscosity. By comparing the rate of CO rebinding to protoheme in glycerol solution with and without a bound proximal imiclazole ligand, we find the enthalpic contribution to the proximal rebinding barrier, Hp, to be 11 +/- 2 kJ/mol. Further comparison of the CO rebinding rate of the imidazole bound protoheme with the analogous rate in myoglobin (Mb) leads to a determination of the difference in their distal free energy barriers: Delta G(D) approximate to 12 +/- 1 kJ/mol. Estimates of the entropic contributions, due to the ligand accessible volumes in the distal pocket and the xenon-4 cavity of myoglobin (similar to 3 kJ/mol), then lead to a distal pocket enthalpic barrier of H-D approximate to 9 +/- 2 kJ/mol. These results agree well with the predictions of a simple model and with previous independent room-temperature measurements (Tian et al. Phys. Rev. Lett. 1992, 68, 408) of the enthalpic MbCO rebinding barrier (18 +/- 2 kJ/mol).
24. Yu, A. C., X. Ye, D. Ionascu, W. X. Cao and P. M. Champion (2005). "Two-color pump-probe laser spectroscopy instrument with picosecond time-resolved electronic delay and extended scan range." Review of Scientific Instruments 76(11): 114301.
An electronically delayed two-color pump-probe instrument was developed using two synchronized laser systems. The instrument has picosecond time resolution and can perform scans over hundreds of nanoseconds without the beam divergence and walk-off effects that occur using standard spatial delay systems. A unique picosecond Ti: sapphire regenerative amplifier was also constructed without the need for pulse stretching and compressing optics. The picosecond regenerative amplifier has a broad wavelength tuning range, which suggests that it will make a significant contribution to two-color pump-probe experiments. To test this instrument we studied the rotational correlation relaxation of myoglobin (tau(r)= 8.2 +/- 0.5 ns) in water as well as the geminate rebinding kinetics of oxygen to myoglobin (k(g1) = 1.7 x 10(11) s(-1), k(g2) = 3.4 x 10(7) s(-1)). The results are consistent with, and improve upon, previous studies. (c) 2005 American Institute of Physics.
25. Zeng, W. Q., N. J. Silvernail, D. C. Wharton, G. Y. Georgiev, B. M. Leu, W. R. Scheidt, J. Y. Zhao, W. Sturhahn, E. E. Alp and J. T. Sage (2005). "Direct probe of iron vibrations elucidates NO activation of heme proteins." Journal of the American Chemical Society 127(32): 11200-11201.
26. Zhang, J. and J. B. Sokoloff (2005). "Adiabatic molecular-dynamics-simulation-method studies of kinetic friction." Physical Review E 71(6): 066125.
An adiabatic molecular-dynamics method is developed and used to study the Muser-Robbins model for dry friction (i.e., nonzero kinetic friction in the slow sliding speed limit). In this model, dry friction between two crystalline surfaces rotated with respect to each other is due to mobile molecules (i.e., dirt particles) adsorbed at the interface. Our adiabatic method allows us to quickly locate interface potential-well minima, which become unstable during sliding of the surfaces. Since dissipation due to friction in the slow sliding speed limit results from mobile molecules dropping out of such unstable wells, our method provides a way to calculate dry friction, which agrees extremely well with results found by conventional molecular dynamics for the same system, but our method is more than a factor of 10 faster.