Caldesmon inhibits both force development and transition of actin monomers from "OFF" to "ON" conformational state by changing its position in thin filaments

We have investigated the effect of caldesmon on the actin conformational state and its position at force generation in glycerinated fibers upon transformation from relaxation to rigor. F-actin and caldesmon were labeled with TRITC-phalloidin or acrylodan, respectively, and the orientation and mobility of the probes were calculated. Transition from relaxation to rigor was accompanied by force development and by the changes in orientation and mobility of TRITC-phalloidin that were typical for actin monomer transformation from the "OFF" to the "ON" conformational state. In the presence of caldesmon, both the force developed by the fibers and the changes in the orientation and mobility of TRITC-phalloidin were markedly decreased. In contrast, the orientation and mobility of acrylodan change essentially showed the displacement of the caldesmon molecules and the changes in its mobility. The results are evidence that structure and/or mode of the attachment of caldesmon to actin modulates both the force production and transition of actin monomers from "OFF" to "ON" conformations in the ATPase cycle.     

Toward a definition of self: proteomic evaluation of the class I peptide repertoire

MHC class I molecules present host- and pathogen-derived peptides for immune surveillance. Much attention is given to the search for viral and tumor nonself peptide epitopes, yet the question remains, "What is self?" Analyses of Edman motifs and of small sets of individual peptides suggest that the class I self repertoire consists of thousands of different peptides. However, there exists no systematic characterization of this self-peptide backdrop, causing the definition of class I-presented self to remain largely hypothetical. To better understand the breadth and nature of self proteins sampled by class I HLA, we sequenced >200 endogenously loaded HLA-B*1801 peptides from a human B cell line. Peptide-source proteins, ranging from actin-related protein 6 to zinc finger protein 147, possessed an assortment of biological and molecular functions. Major categories included binding proteins, catalytic proteins, and proteins involved in cell metabolism, growth, and maintenance. Genetically, peptides encoded by all chromosomes were presented. Statistical comparison of proteins presented by class I vs the human proteome provides empiric evidence that the range of proteins sampled by class I is relatively unbiased, with the exception of RNA-binding proteins that are over-represented in the class I peptide repertoire. These data show that, in this cell line, class I-presented self peptides represent a comprehensive and balanced summary of the proteomic content of the cell. Importantly, virus- and tumor-induced changes in virtually any cellular compartment or to any chromosome can be expected to be presented by class I molecules for immune recognition.     

Solid state structural analysis of the cyclooctapeptide cyclo- (Pro1-Pro-Phe-Phe-Ac6c-Ile-D-Ala-Val8)

A solid state analysis of the cyclic octapeptide c(-Pro(1)-Pro-Phe-Phe-Ac(6)c-Ile-D-Ala-Val(8)-) (C8-CLA), containing the Pro-Pro-Phe-Phe sequence, followed by the bulky helicogenic C(alpha,alpha)-dialkylated 1-aminocyclohexane-1-carboxylic acid (Ac(6)c) residue and a D-Ala residue in position 7, has been carried out by x-ray diffraction.The crystals, grown from a DMSO solution, are monoclinic, space group P2(1) with a = 13.458(3) A, b = 19. 404(5) A, c = 21.508(4) A, and beta = 90.83(6) degrees, with two independent cyclic molecules in the asymmetric unit, two DMSO molecules, and three water molecules. The structure has been solved using the half and bake procedure by Sheldrick, and refined to final R1 and wR2 indices of 0.0613 and 0.1534 for 9867 reflections with I > 2sigma(I).This cyclic peptide, a deletion analogue of the naturally occurring cyclic nonapeptide cyclolinopeptide A [c(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val), CLA] has been designed to study the influence of the ring size reduction on the conformational behavior of CLA and more in general to obtain structural information on asymmetric cyclic octapeptides.The compound exhibits, in the solid state, a "banana-twisted" conformation with a cis peptide bond located between the two proline residues. Five intramolecular H bonds stabilize the structure: one type VIa beta-turn, two consecutive type III/I beta-turns, one gamma-turn, and one C(16) bend.The structure has also been compared with either the solution structure previously reported by us and obtained by nmr and computational analysis, and with solid state structural data reported in the literature on cyclic octapeptides.     

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer

In cellular respiration, cytochrome c transfers electrons from cytochrome bc(1) complex (complex III) to cytochrome c oxidase by transiently binding to the membrane proteins. Here, we report the structure of isoform-1 cytochrome c bound to cytochrome bc(1) complex at 1.9 A resolution in reduced state. The dimer structure is asymmetric. Monovalent cytochrome c binding is correlated with conformational changes of the Rieske head domain and subunit QCR6p and with a higher number of interfacial water molecules bound to cytochrome c(1). Pronounced hydration and a "mobility mismatch" at the interface with disordered charged residues on the cytochrome c side are favorable for transient binding. Within the hydrophobic interface, a minimal core was identified by comparison with the novel structure of the complex with bound isoform-2 cytochrome c. Four core interactions encircle the heme cofactors surrounded by variable interactions. The core interface may be a feature to gain specificity for formation of the reactive complex.     

Water transport and ion-water interaction in the gramicidin channel

The diffuse permeability and the diffusion coefficient of water (Dw) in the gramicidin channel is determined from the osmotic water permeability of the channel and "single file" pore theory. Dw is about 7% of the self-diffusion coefficient of bulk water. The diffusion coefficient of a single water molecule alone in the channel is also determined and is about equal to the value in bulk water. This provides an estimate of the mobility of water on the channel walls in the absence of water-water interaction. Since the gramicidin channel walls should be representative of uncharged polar protein surfaces, this result provides direct evidence that the presence of a cation in the channel reduces the hydraulic water permeability by a factor ranging from 60 for Tl+ to 5 for Na+. The diffusion coefficient of a cation (Dc) in the channel is estimated and compared with Dw. For Na+ it is found that Dc approximately equal to Dw, which implies that the movement of the row of water molecules through the channel determines the local mobility of Na+. Thus, it seems that short range ion-wall interactions are not important in determining the channel conductance for Na+. In contrast, for Li+, local ion-wall interactions probably do limit the conductance.     

A model for the simulation of an aqueous dipeptide solution

A model for the simulation of a solution of an alanine dipeptide in water is presented that combines a previous model for bulk water (ST2) with that used in conformational energy studies on small molecules and proteins. The results of a pilot molecular dynamics study indicate that the model leads to reasonable solvent–solute interactions. No evidence is found for substantial changes in the structure or dynamics of the dipeptide in solution as compared to in vacuo. Furthermore, at the elevated temperature examined, there appear to be no significant effects on the dynamics or intermolecular bonding of the water molecules in contact with the solute.     

Interpreting the equatorial diffraction pattern of collagenous tissues in the light of molecular motion.

The equatorial diffraction pattern associated with collagenous tissues, particularly type I collagen, is diffuse and clearly unlike that from crystals. Hukins and Woodhead-Galloway proposed a statistical model that they termed a "liquid crystal" for collagen fibers in tendons. Fratzl et al. applied this model to both unmineralized and mineralized turkey leg tendon, a model that ignores the organization imposed by the well-known cross-linking. The justification for adopting this model is that the curve fits the data. It is shown that the data can be equally well matched by fitting a least-squares curve consisting of a second-order polynomial plus a Gaussian. The peak of the Gaussian is taken as the equatorial spacing of the collagen. A physical explanation for this model is given, as is a reason for the changes in the spacing with changes in water content of the tissue. The diffusion is attributed to thermally driven agitation of the molecules, in accordance with the Debye-Waller theory including the Gaussian distribution. The remainder of the diffusion is attributed to other scattering sources like the mineral crystallites.     

Nonspecific effect of morphine on the erythrocyte membrane

The effect of low morphine concentrations on the plasmatic membranes of erythrocytes without opiate receptors was investigated. It was shown that the ATPase activity and hemolytic stability of erythrocytes, which characterize the state of cell membranes and the mobility of the near-membrane water phase, depend on the concentration of morphine, and this dependence is wave-like. The nonmonotonous dependence of the biological response was suggested to be due to changes in the structure of water hydrogen links near the membrane surface, induced by opiate molecules. The hypothesis was confirmed by the results of studies of morphine water solutions using the methods of fluorescent probe and light scattering. It was found that the intensity of light scattering by water and the mobility of its molecules considerably increase in the presence of strictly specified concentrations of morphine.     

The cellular resting and action potentials: interpretation based on the association-induction hypothesis

The Hodgkin, Huxley, and Katz theories of resting and action potentials are based on the membrane theory, which holds that cell K+ and water exist in the free state. Reviewed here are these theories of cellular potential along with the results of experimental testings. Reviewed also is Ling's association-induction (AI) hypothesis, which holds that all K+ is absorbed selectively and singly on anionic protein sites and that cell water is absorbed in multilayers on extended chains of "matrix proteins." In the development of the AI model, molecular mechanisms of cell permeation and electric potentials were presented according to which the potentials are surface-adsorption phenomena. Thus they resemble those suggested by Baur rather than the membrane potentials proposed by Ostwald and Bernstein. In the present review it is shown that the AI version of the surface adsorption model can account for evidence supporting the Hodgkin, Huxley, Katz approach as well as evidence against it-including extensive recent confirmation of the absorbed state of K+ in muscle.     

A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate

Asparagine 131, located near the cytoplasmic entrance of the D-pathway in subunit I of the Paracoccus denitrificans aa(3) cytochrome c oxidase, is a residue crucial for proton pumping. When replaced by an aspartate, the mutant enzyme is completely decoupled: while retaining full cytochrome c oxidation activity, it does not pump protons. The same phenotype is observed for two other substitutions at this position (N131E and N131C), whereas a conservative replacement by glutamine affects both activities of the enzyme. The N131D variant oxidase was crystallized and its structure was solved to 2.32-A resolution, revealing no significant overall change in the protein structure when compared with the wild type (WT), except for an alternative orientation of the E278 side chain in addition to its WT conformation. Moreover, remarkable differences in the crystallographically resolved chain of water molecules in the D-pathway are found for the variant: four water molecules that are observed in the water chain between N131 and E278 in the WT structure are not visible in the variant, indicating a higher mobility of these water molecules. Electrochemically induced Fourier transform infrared difference spectra of decoupled mutants confirm that the protonation state of E278 is unaltered by these mutations but indicate a distinct perturbation in the hydrogen-bonding environment of this residue. Furthermore, they suggest that the carboxylate side chain of the N131D mutant is deprotonated. These findings are discussed in terms of their mechanistic implications for proton routing through the D-pathway of cytochrome c oxidase.     

Effect of solvent diffusion on the apomyoglobin-water interface

Few techniques can identify interactions between proteins and individual water molecules when the protein is in solution. The present work has sought to bridge the gap between the molecular level studies and the search for a physical property of the solution (bathing the proteins) that would regulate the protein hydration level. The properties of the solution were varied by adding nondenaturing solutes and solvents to the protein solutions and then studying their effect on the intrinsic fluorescence of apomyoglobin. The resolution of the tryptophan emission into the two component spectra corresponding to tryptophans W7 (accessible to the solvent) and W14 (buried in the protein matrix) has allowed us to probe two specific parts of the protein. Whereas W14 is not affected when the medium is altered, the analysis of W7 fluorescence has shown that cosolvent diffusion plays a dominant role in the mobility of water molecules near the protein surface.     

Influence of the fluidity of the membrane on the response of microorganisms to environmental stresses

The aim of this mini-review is to relate membrane physical properties to the adaptation and resistance of microorganisms to environmental stresses. In the first part, the effects of various stresses on the structure and dynamic properties of phospholipid and biological membranes are presented. The compensation of these effects, i.e., change in membrane fluidity, phase transitions, by the active cellular control of the membrane chemical composition, is then described. In this natural process, the change in membrane fluidity is viewed as the detecting "input" signal that initiates the regulation, activating proteic effectors that in turn may influence the chemical composition of the membrane (feedback). This adaptation system allows the maintenance of the physical characteristics of membranes and, thereby, of their functionality. When environmental stresses are extreme and occur abruptly, the regulation process may not compensate for the changes in the membrane physical characteristics. In such cases, important variations in the membrane fluidity and structure may induce cellular damages and cell death. However, the lethal consequences are not systematically observed because protective effects of changes in the membrane physical state on the resistance to stresses are also reported.     

Generalized stern models of the electric double layer considering the spatial variation of permittvity and finite size of ions in saturation regime

The interaction between a charged metal implant surface and a surrounding body fluid (electrolyte solution) leads to ion redistribution and thus to formation of an electrical double layer (EDL). The physical properties of the EDL contribute essentially to the formation of the complex implant-biosystem interface. Study of the EDL began in 1879 by Hermann von Helmholtz and still today remains a scientific challenge. The present mini review is focused on introducing the generalized Stern theory of an EDL, which takes into account the orientational ordering of water molecules. To ascertain the plausibility of the generalized Stern models described, we follow the classical model of Stern and introduce two Langevin models for spatial variation of the relative permittivity for point-like and finite sized ions. We attempt to uncover the subtle interplay between water ordering and finite sized ions and their impact on the electric potential near the charged implant surface. Two complementary effects appear to account for the spatial dependency of the relative permittivity near the charged implant surface — the dipole moment vectors of water molecules are predominantly oriented towards the surface and water molecules are depleted due to the accumulation of counterions. At the end the expressions for relative permittivity in both Langevin models were generalized by also taking into account the cavity and reaction field.     

Low-Moisture Food: A Physicochemical Approach to Investigate the Origin of Their Physical Instability versus Water or Sucrose

Low-moisture biopolymer-based systems are commonly encountered in food. Obviously, understanding the physical basis of their quality [texture, or performance over time or as a function of their composition (water or other added solutes)] is of primary importance. A polymer science approach using physical chemistry concepts based on physical state, phase transitions and molecular mobility can be applied to investigate the performances of food in particular versus moisture. Based on the example of starch-based samples and their texture property changes versus composition, the role of water and sucrose is considered through different aspects. The relations existing between the observed changes and physical state are investigated. While the motions associated with the glass transition were observed at high temperature, secondary relaxations are observed below Tg (at T _β): T _β decreased with water content and increased with increasing sucrose content. These local motions are suggested to contribute to the observed texture modifications versus water. Moreover, the stability of the glassy state was investigated by differential scanning calorimetry through the study of enthalpy relaxation (physical ageing). The amplitude of enthalpy relaxation decreased with both increasing sucrose and water content. All in all, this study strengthened the hypotheses that sub-Tg mobility could contribute to texture instability versus moisture or sugar content.     

Influence of sucrose and water content on molecular mobility in starch-based glasses as assessed through structure and secondary relaxation

Molecular mobility is known to be a key parameter in controlling the physical properties of materials and thus their quality and performance. Beyond glass transition related changes, attention should be called to the impact of local motions remaining in the glassy state. Gelatinized waxy maize starch at different sucrose contents (0-20% solids) was equilibrated between 0 and 14% water and sorption isotherms determined at 25 degrees C. The effect of water and sucrose content on the molecular mobility of glassy starch was investigated by differential scanning calorimetry through enthalpy relaxation studies and dynamical mechanical thermal analysis. The existence of sucrose-starch interactions was suggested by the sorption isotherms not following the expected additivity of the single component sorption curves. Contrary to the glass transition or associated alpha relaxation, water and sucrose affected differently the secondary relaxations. Indeed, the beta relaxation observed around -15 degrees C was shifted to lower temperature upon increasing hydration, and to higher temperature when sucrose content increased, suggesting a hindering of these local motions. Enthalpy relaxation of the ternary mixtures was studied following aging up to 668 h at Tg -15 degrees C. Ternary mixtures exhibited an enthalpy relaxation upon aging lower than starch alone as a sign of lower polymer mobility in the presence of small molecules, contrary to the free volume theory. Relaxation kinetics were characterized with the Cowie-Ferguson model and compared to literature data. The extent of the enthalpy relaxation appeared to be controlled by the distance between the aging temperature and the beta relaxation temperature.     

Solvent effects on the cooperative order-disorder transition of aqueous solutions of schizophyllan, a triple-helical polysaccharide

A triple helical polysaccharide schizophyllan in aqueous solution exhibited a highly cooperative transition between ordered and disordered states associated with the conformation of its side chains and nearby water molecules. The transition was followed by optical rotation and calorimetry using water containing additives such as NaOH and DMSO as solvents. The ordered state was stabilized or destabilized depending on the kind and amount of the additive employed; in particular, the addition of DMSO had a remarkable stabilizing effect. This effect was analyzed by means of a statistical mechanical theory of linear cooperative transitions, where DMSO was assumed to interact favorably with the ordered side chains. A small amount of NaOH in a solvent mixture stabilized the ordered state and made the transition curve very gradual. No molecular mechanism was elucidated to account for the role of NaOH.     

Water in protein hydration and ligand recognition

This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.     

Ion homeostasis and the functional roles of SERCA reactions in stimulus-secretion coupling of the pancreatic beta-cell: A mathematical simulation

The present paper concerns with ion homeostatic reactions in view of stimulus-secretion coupling of the beta-cell, including Ca2+ fluxes of the endoplasmatic reticulum (ER). A steady state of cytosolic sodium and potassium ion concentrations ([Na+]c and [K+]c, respectively), and of the membrane potential (Delta c phi) can be attained only, if the flux through the electrogenic Na-K pump (JNaK) is balanced electrically, and if JNaK is rather high (about 25% of total ATP consumption at 10 mM glucose). Metabolically caused changes of cellular pH are unlikely, because, on the one hand, CO2 can rapidly leave the cell through cellular membranes, and because ATP cycling cannot produce nor consume protons. A slight decrease of pHc during cellular activity is caused mainly by an increased Ca-H exchange flux through the plasma membrane Ca2+ pump (J PMCA), which might be overcome, however, by H+ transport into secretory granules. The present simulations show that the conductance of ATP-sensitive K+ channels (K ATP) is highly susceptible to changes of [Mg2+]c. As a physical link between the Ca2+ filling state of the ER and the initiation of a depolarising, Ca2+ release-activated current (I CRAN), a metabolite (inositol 1,4,-diphosphate (IP2)) of the inositol 1,4,5-triphosphate (IP3) cycle is introduced. Sufficient ATP for insulin secretion is made available during glucose activation by [IP2] inhibition of a parallel [ATP]c consuming flux through protein biosynthesis (J Pbs). This leads to fast oscillations with a triphasic patterns of [Ca2+]c oscillations. Slow oscillations are initiated by including a Ca2+ leak current through highly uncoupled SERCA3 pumps. Both types of oscillations may superimpose yielding compound bursting and mixed oscillations of [Ca2+]c.     

Cellular functions of a cell in a metastable equilibrium state

A unifying hypothesis which might replace some of the many ion pumps which are invoked to describe distribution of ions across living cell membranes is developed quantitatively. Resting cells are assumed to be in a metastable state such that ions are in equilibrium between an extracellular aqueous phase, in which water has the properties of the bulk liquid, and an intracellular aqueous phase in which water has enhanced structure and strongly modified solvent properties. Partition coefficients or medium effects for Na⁺, K⁺ and Cl⁻ are calculated for several cell types. It is shown that in such a hypothetical cell, possessing no ion pumps there is an amplified Donnan potential between the two phases, its sign determined by the net charge on intracellular proteins, and its magnitude increased by a separation of ions induced by the difference in solvent properties of the water in the two phases. It is shown that a cell in such a metastable state is excitable and can generate an action potential with an inward surge of Na+ followed by an outward surge of K+. An explanation is offered for the transient release of Caa+ from the sarcoplasmic reticulum following excitation of a muscle fibre. Regulation of cellular volume is shown to be a necessary result of the presence in the extracellular solution of a high concentration of Na+, an ion with a very low affinity for intracellular water. It is concluded that the principal cellular functions that are commonly attributed to the sodium pump are also a feature of a cell in a metastable equilibrium state.     

The chemical characterization of the gene: vicissitudes of evidential assessment

The chemical characterization of the substance responsible for the phenomenon of "transformation" of pneumococci was presented in the now famous 1944 paper by Avery, MacLeod, and McCarty. Reception of this work was mixed. Although interpreting their results as evidence that deoxyribonucleic acid (DNA) is the molecule responsible for genetic changes was, at the time, controversial, this paper has been retrospectively celebrated as providing such evidence. The mixed and changing assessment of the evidence presented in the paper was due to the work's interpretive flexibility--the evidence was interpreted in various ways, and such interpretations were justified given the neophytic state of molecular biology and methodological limitations of Avery's transformation studies. I argue that the changing context in which the evidence presented by Avery's group was interpreted partly explains the vicissitudes of the assessments of the evidence. Two less compelling explanations of the reception are a myth-making account and an appeal to the wartime historical context of its publication.