Water and ligand entry in myoglobin: assessing the speed and extent of heme pocket hydration after CO photodissociation

A previously undescribed spectrokinetic assay for the entry of water into the distal heme pocket of wild-type and mutant myoglobins is presented. Nanosecond photolysis difference spectra were measured in the visible bands of sperm whale myoglobin as a function of distal pocket mutation and temperature. A small blue shift in the 560-nm deoxy absorption peak marked water entry several hundred nanoseconds after CO photodissociation. The observed rate suggests that water entry is rate-limited by the escape of internal dissociated CO. The heme pocket hydration and geminate recombination yields were found to be the primary factors controlling the overall bimolecular association rate constants for CO binding to the mutants studied. The kinetic analysis provides estimates of 84%, 60%, 40%, 0%, and 99% for the steady-state hydrations of wild-type, H64Q, H64A, H64L, and V68F deoxymyoglobin, respectively. The second-order rate constants for CO and H(2)O entry into the empty distal pocket of myoglobin are markedly different, 8 x 10(7) and 2 x 10(5) M(-1).s(-1), respectively, suggesting that hydrophobic partitioning of the apolar gas from the aqueous phase into the relatively apolar protein interior lowers the free energy barrier for CO entry.     

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is "dynamical fingerprints" which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.     

Nonexponential protein relaxation: dynamics of conformational change in myoglobin.

The picosecond evolution of the tertiary conformation of myoglobin (Mb) after photodissociation of MbCO was investigated at room temperature by probing band III, a weak iron-porphyrin charge-transfer transition near 13,110 cm-1 (763 nm) that is sensitive to the out-of-plane displacement of the iron. Upon photolysis, the iron moves out of the plane of the porphyrin, causing a blue-shift of band III and a concomitant change in the protein conformation. The dynamics for this functionally important motion are highly nonexponential, in agreement with recent molecular dynamics simulations [Kuczera, K., Lambry, J.-C., Martin, J.-L. & Karplus, M. (1993) Proc. Natl. Acad. Sci. USA 90, 5805-5807]. The conformational change likely affects the height of the barrier to ligand rebinding and may explain nonexponential NO rebinding.     

Subpicosecond oxygen trapping in the heme pocket of the oxygen sensor FixL observed by time-resolved resonance Raman spectroscopy

Dissociation of oxygen from the heme domain of the bacterial oxygen sensor protein FixL constitutes the first step in hypoxia-induced signaling. In the present study, the photodissociation of the heme-O2 bond was used to synchronize this event, and time-resolved resonance Raman (TR(3)) spectroscopy with subpicosecond time resolution was implemented to characterize the heme configuration of the primary photoproduct. TR(3) measurements on heme-oxycomplexes are highly challenging and have not yet been reported. Whereas in all other known six-coordinated heme protein complexes with diatomic ligands, including the oxymyoglobin reported here, heme iron out-of-plane motion (doming) occurs faster than 1 ps after iron-ligand bond breaking; surprisingly, no sizeable doming is observed in the oxycomplex of the Bradyrhizobium japonicum FixL sensor domain (FixLH). This assessment is deduced from the absence of the iron-histidine band around 217 cm(-1) as early as 0.5 ps. We suggest that efficient ultrafast oxygen rebinding to the heme occurs on the femtosecond time scale, thus hindering heme doming. Comparing WT oxy-FixLH, mutant proteins FixLH-R220H and FixLH-R220Q, the respective carbonmonoxy-complexes, and oxymyoglobin, we show that a hydrogen bond of the terminal oxygen atom with the residue in position 220 is responsible for the observed behavior; in WT FixL this residue is arginine, crucially implicated in signal transmission. We propose that the rigid O2 configuration imposed by this residue, in combination with the hydrophobic and constrained properties of the distal cavity, keep dissociated oxygen in place. These results uncover the origin of the "oxygen cage" properties of this oxygen sensor protein.     

Perturbations of the distal heme pocket in human myoglobin mutants probed by infrared spectroscopy of bound CO: correlation with ligand binding kinetics.

The infrared spectra of CO bound to human myoglobin and myoglobin mutants at positions His-64, Val-68, Asp-60, and Lys-45 on the distal side have been measured between 100 and 300 K. Large differences are observed with mutations at His-64 and Val-68 as well as with temperature and pH. Although distal His-64 is found to affect CO bonding, Val-68 also plays a major role. The variations are analyzed qualitatively in terms of a simple model involving steric interaction between the bound CO and the distal residues. A strong correlation is found between the final barrier height to CO recombination and the CO stretch frequency: as compared to wild type, the barrier is smaller in those mutants that have a higher CO stretch frequency (vCO) and vice versa. Possible reasons for this correlation are discussed. It is emphasized that the temperature and pH dependence of both the kinetics and the infrared spectra must be measured to obtain a consistent picture.     

Energy barriers in binding of carbon monoxide and oxygen to heme model compounds.

Binding of carbon monoxide and oxygen to sterically protected heme model compounds (basket-handle porphyrins) was investigated in liquid toluene at temperatures from 180 to 300 K by laser flash photolysis. Only a single exponential rebinding process from the solvent could be seen in the time range of 20 nsec to milliseconds. The fraction of ligands that initially escaped into the solvent decreased when the temperature was lowered, and the Arrhenius plots for the rebinding rate coefficients were found to deviate significantly from linearity. These findings suggest that protected heme model compounds might react according to a double energy-barrier scheme. In contrast, the reaction of an unprotected porphyrin can be described by a single energy barrier.     

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis

The structural and mechanical properties of monomeric actin (G-actin), the trimer nucleus, and actin filaments (F-actins) are determined as a function of the conformation of the DNase I-binding loop (DB loop) by using all-atom molecular dynamics simulations and coarse-grained (CG) analysis. Recent x-ray structures of ADP-bound G-actin (G-ADP) by Otterbein et al. [Otterbein, L. R., Graceffa, P. & Dominguez, R. (2001) Science 293, 708-711] and ATP-bound G-actin (G-ATP) by Graceffa and Dominguez [Graceffa, P. & Dominguez, R. (2003) J. Biol. Chem. 278, 34172-34180] indicate that the DB loop of actin does not have a well defined secondary structure in the ATP state but folds into an alpha-helix in the ADP state. MD simulations and CG analysis indicate that such a helical DB loop significantly weakens the intermonomer interactions of actin assemblies and thus leads to a wider, shorter, and more disordered filament. The computed persistence lengths of F-actin composed of G-ATP (16 microm) and of G-ADP (8.5 microm) agree well with the experimental values for the two states. Therefore, the loop-to-helix transition of the DB loop may be one of the factors that lead to the changes in structural and mechanical properties of F-actin after ATP hydrolysis. This result may provide a direct connection between the conformational changes of an actin monomer and the structural and mechanical properties of the cytoskeleton. The information provided by MD simulations also helps to understand the possible origin of the special features of actin dynamics.     

HO-CO系统在糖尿病足患者中的表达及其意义

目的探讨血红素氧化酶-一氧化碳系统（HO-CO）与糖尿病足（DF）发病的关系。方法DF组30例，单纯糖尿病（DM）组25例，对照（NC）组25例，测定血浆CO浓度，用免疫组织化学法观察足部组织中HO-1、HO-2的表达。结果（1）DF组较DM组病程长，FPG、HbA1 c升高，TG、血浆CO浓度降低（P〈0．05）。（2）DF组较DM组HO-1、HO-2表达明显减弱（P〈0．01）。（3）血浆CO浓度与FPG呈显著负相关关系（P〈0．01）结论DM患者HO-CO系统表达的减弱可能在DF的发生发展中起重要作用，高血糖可能是影响HO-CO系统的主要因素。     

Influence of capillary and tissue PO2 on carbon monoxide binding to myoglobin: A theoretical evaluation

In order to evaluate how much myoglobin is linked to CO at various HbCO concentrations and at different P_O2, a three compartment model (arterial blood, venous capillary blood, and tissue myoglobin) has been considered. A steady-state condition has been assumed for O₂ consumption with no metabolization for CO. The curves obtained by computer simulation of the proposed model indicate that HbCO levels found in smokers entail values of MbCO which could be high enough to reduce intracellular oxygen transport significantly: especially where the P_O2 is physiologically low (as in subendocardium) and/or hypoxemic-ischemic conditions are present.     

实验性肝损伤大鼠肝脏HO-1的表达及CO水平变化

目的研究急性肝损伤时大鼠肝脏HO-1的表达情况和CO水平,探讨HO-1和内源性CO在大鼠急性肝损伤中的作用.方法制备急性四氯化碳肝损伤模型,采用RT-PCR和免疫组化法测定不同时间点大鼠肝脏HO-1 mRNA和蛋白的表达情况;测定各时间点肝组织SOD、MDA含量变化,同时测定股静脉血中HbCO水平和ALT、AST肝功能指标.结果HO-1mRNA在正常大鼠有弱表达,染毒3 h后表达显著增强,于24 h时间点表达最强,与对照组相比差异非常显著(P＜0.01);免疫组化结果显示;HO-1蛋白在正常大鼠表达较低或无,染毒3h后即有明显表达,16至48h的时间点内表达均显著增强,主要定位于肝实质细胞、库普细胞的胞浆内.对照组HbCO水平极低,给予四氯化碳3 h后HbCO水平开始升高,此后各时间点均明显高于对照组,差异有显著性,这与HO-1表达情况相一致.此外,染毒后大鼠血清ALT、AST和MDA明显升高,SOD活性则显著降低,和对照组相比差异均十分显著.结论大鼠急性肝损伤后出现HO-1表达持续上调和血中CO水平迅速增高,提示HO/CO系统参与急性肝损伤的病理生理过程,其表达增加可能对机体有重要调节作用.     

Kinetics of oxygen and carbon monoxide binding to synthetic analogs of the myoglobin and hemoglobin active sites.

Kinetics of reversible oxygenation and carbon monoxide complex formation of the simple heme compounds pyrroheme-N-[3-(1-imidazolyl)propyl]amide and pyrroheme-3-(3-pyridyl)propyl ester have been measured in different solvent environments. The oxygen on and off rates and equilibria of these compounds can be made to closely match those of myoglobin, of hemoglobin alpha chains, or of the various steps for hemoglobin by varying solvent environment or the basicity of the proximal base. These results suggest that the protein could alter oxygen on rates by varying the basicity of the proximal base and the off rates by changing the polarity of the distal environment.     

家兔动脉粥样硬化进程中内皮依赖性因子的变化及其相互关系研究

目的　探讨血红素氧合酶-1(HO -1) /一氧化碳(CO)系统与一氧化氮合酶(NOS) /一氧化氮(NO)在动脉粥样硬化中的变化、相互关系及对动脉粥样硬化进程的影响。方法　家兔予以高胆固醇饮食(n=8)以及在高胆固醇饮食的同时经饮水给予L -精氨酸(n=8)或亚硝基左旋精氨酸甲酯(n=8),或经腹腔注射血红素L -赖氨酸盐(n=8)或锌原卟啉9 (ZnPP- IX) (n=8 ),共10周。结果与对照组比较,胆固醇组主动脉NO生成量显著减少,CO生成则明显增加,NOS活性显著降低(P均<0 .01),而HO -1表达升高,主动脉斑块面积达(40. 2±8 .9)% 。与胆固醇组比较,外源性血红素L -赖氨酸盐干预组的主动脉内膜斑块面积[ (26. 6±9 .2)% ]明显缩小,主动脉CO的生成量和HO- 1表达明显升高(P<0. 01),但NOS活性与NO产量较正常对照组显著降低(P<0 .01),与胆固醇组比较则无显著差异;与胆固醇组比较,外源性L 精氨酸显著升高主动脉cNOS活性,增加NO生成量,主动脉斑块面积[ (28. 1±7 .7)% ]明显缩小(P均<0. 01),而HO -1的表达和CO的生成较正常对照组显著升高,与胆固醇组相比差异无统计学意义。与胆固醇组比较,血红素L 赖氨酸盐干预组、L 精氨酸组的主动脉组织内c- myc及c- fos的mRNA和蛋白表达均显著降低,而ZnPP组和亚硝基左旋精氨酸甲酯组则无明显差异。结论　动     

Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines

Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well defined internal mechanical motions to various initial deformations and that these motions are robust against external perturbations. We show that this behavior is not characteristic for random elastic networks. However, special network architectures with such properties can be designed by evolutionary optimization methods. Using them, an example of an artificial elastic network, operating as a cyclic machine powered by ligand binding, is constructed.     

The role of carbon monoxide and heme oxygenase in the prevention of sickle cell disease vaso‐occlusive crises

Sickle Cell Disease (SCD) is a painful, lifelong hemoglobinopathy inherited as a missense point mutation in the hemoglobin (Hb) beta‐globin gene. This disease has significant impact on quality of life and mortality, thus a substantial medical need exists to reduce the vaso‐occlusive crises which underlie the pathophysiology of the disease. The concept that a gaseous molecule may exert biological function has been well known for over one hundred years. Carbon monoxide (CO), although studied in SCD for over 50 years, has recently emerged as a powerful cytoprotective biological response modifier capable of regulating a host of physiologic and therapeutic processes that, at low concentrations, exerts key physiological functions in various models of tissue inflammation and injury. CO is physiologically generated by the metabolism of heme by the heme oxygenase enzymes and is measurable in blood. A substantial amount of preclinical and clinical data with CO have been generated, which provide compelling support for CO as a potential therapeutic in a number of pathological conditions. Data underlying the therapeutic mechanisms of CO, including in SCD, have been generated by a plethora of in vitro and preclinical studies including multiple SCD mouse models. These data show CO to have key signaling impacts on a host of metallo‐enzymes as well as key modulating genes that in sum, result in significant anti‐inflammatory, anti‐oxidant and anti‐apoptotic effects as well as vasodilation and anti‐adhesion of cells to the endothelium resulting in preservation of vascular flow. CO may also have a role as an anti‐polymerization HbS agent. In addition, considerable scientific data in the non‐SCD literature provide evidence for a beneficial impact of CO on cerebrovascular complications, suggesting that in SCD, CO could potentially limit these highly problematic neurologic outcomes. Research is needed and hopefully forthcoming, to carefully elucidate the safety and benefits of this potential therapy across the age spectrum of patients impacted by the host of pathophysiological complications of this devastating disease.     

From the Cover: High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations.Structured RNAs exhibit a distinct preference for loops of precisely 4 nt, which was originally noted by Woese et al. (1) using comparative sequence analysis of ribosomes. Approximately 70% of these tetraloops are comprised of just three specific loop sequences: UUCG, GCAA, or CUUG. The abundance of these sequences is thermodynamic in origin, because each motif forms a unique network of noncanonical interactions within their loops that stabilizes the folded state. The abundance of high-resolution structural and thermodynamic data available for these motifs coupled with their characteristic noncanonical signatures make them ideal for adjudicating the accuracy of RNA folding simulations.RNA folding is understood to be hierarchical in nature, with secondary and tertiary folds stabilized by distinct thermodynamic driving forces (2). Secondary structure (the formation of canonical helices stabilized by Watson–Crick base pairs) can be accurately predicted from the nucleotide sequence alone using simple nearest neighbor thermodynamic models (3). In contrast, tertiary structure formation is a subtle competition between intrinsic flexibility of single-stranded segments, rigidity imparted from base-stacking interactions, stabilization of noncanonical hydrogen bonding patterns, and site-specific ion binding. In principle, a molecular dynamics simulation using a properly calibrated force field should capture all of the physicochemical properties of ribonucleotides relevant to the RNA folding process. Up until now, however, even small, fast-folding tetraloops cannot be accurately and reversibly folded from the unfolded state (4–6). In contrast, numerous documented successes have been reported using de novo protein folding with all-atom molecular dynamics simulations (7).In this work, we present the results of replica exchange molecular dynamics (REMD) simulations that are consistently able to correctly fold all three hyperstable tetraloops from random unfolded states to 1–3 Å rmsd from their experimentally determined structures, using optimized RNA parameters. These parameters feature van der Waals interactions that have been calibrated against high-level quantum mechanics (QM) dispersion calculations in conjunction with a suite of experimental measurements of aqueous nucleoside and dinucleotide interactions. The resulting RNA parameters reproduce the experimentally measured clustering propensities of aqueous nucleoside solutions as a function of concentration, the thermodynamics of base stacking as a function of temperature, and the population and lifetimes of syn-anti glycosidic transitions; in contrast, we find that the default AMBER-99 RNA (8) parameters fail all of these same tests. We find that these degrees of freedom are intrinsically coupled and that only a simultaneous global reparameterization results in the ability to reversibly fold hyperstable tetraloops with their signature noncanonical interactions. The ability to fold small model RNAs de novo enables future computational studies of larger biologically interesting RNAs, such as riboswitches, ribozymes, and mRNA UTRs.     

Nonlinearity in bacterial population dynamics: Proposal for experiments for the observation of abrupt transitions in patches

An explicit proposal for experiments leading to abrupt transitions in spatially extended bacterial populations in a Petri dish is presented on the basis of an exact formula obtained through an analytic theory. The theory provides accurately the transition expressions despite the fact that the actual solutions, which involve strong nonlinearity, are inaccessible to it. The analytic expressions are verified through numerical solutions of the relevant nonlinear equation. The experimental setup suggested uses opaque masks in a Petri dish bathed in ultraviolet radiation [Lin A-L, et al. (2004) Biophys J 87:75–80 and Perry N (2005) J R Soc Interface 2:379–387], but is based on the interplay of two distances the bacteria must traverse, one of them favorable and the other adverse. As a result of this interplay feature, the experiments proposed introduce highly enhanced reliability in interpretation of observations and in the potential for extraction of system parameters.     

Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data

Transfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA-tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free tRNA with the cryo-EM map of P/E-tRNA. In our approach, we show that the cryo-EM map may be interpreted as a conformational average. Along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of the snapshots prove to be quite close to the observed density. In a representative structure, the CCA (3') arm is uniquely twisted, and the anticodon stem loop is kinked at the junctions to both the anticodon loop and the D stem. In addition, the map shows that the P/E-tRNA is no longer bound to helix H69 of 23S rRNA and is flexible, and the conformations of helices H68 and h44 of 16S rRNA differ from those in the x-ray structure. Thus, our study presents structural and dynamic information on the P/E-tRNA and characterizes its interactions with the translocating ribosome.