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PubMed1997

A mutation in E. coli SSB protein (W54S) alters intra-tetramer negative cooperativity and inter-tetramer positive cooperativity for single-stranded DNA binding.

E. coli SSB tetramer binds with high affinity and cooperatively to single-stranded (ss) DNA and functions in replication, recombination and repair. Curth et al. (Biochemistry, 32 (1993) 2585-2591) have shown that a mutant SSB protein, in which Trp-54 has been replaced by Ser (W54S) in each subunit, binds preferentially to ss-polynucleotides in the (SSB)35 mode in which only 35 nucleotides are occluded per tetramer under conditions in which wild-type (wt) SSB binds in its (SSB)65 mode. The W54S mutant also displays increased UV sensitivity and slow growth phenotypes, suggesting defects in vivo in both repair and replication (Carlini et al. (Molecular Microbiology, 10 (1993) 1067)). We have characterized the energetics of SSBW54S binding to poly(dT) as well as short oligodeoxyribonucleotides (dA(pA)69, dT(pT)34, dC(pC)34) to determine the basis for this dramatic change in binding mode preference. We find that the W54S mutant remains a stable tetramer; however, its affinity for ss-DNA as well as both the intra-tetramer negative cooperativity and its inter-tetramer positive cooperativity in the (SSB)35 mode (omega 35) are altered significantly compared to wtSSB. The increased intra-tetramer negative cooperativity makes it more difficult for ss-DNA to bind the third and fourth subunits of the W54S tetramer, explaining the increased stability of the (SSB)35 mode in complexes with poly(dT). When bound to dA(pA)69 in the (SSB)35 mode, W54S tetramer also displays a dramatically lower inter-tetramer positive cooperativity (omega 35 = 77(+/-20)) than wtSSB (omega 35 > or = 10(5)) as well as a significantly lower affinity for ss-DNA. These results indicate that a single amino acid change can dramatically influence the ability of SSB tetramers to bind in the different SSB binding modes. The altered ss-DNA properties of the W54S SSB mutant are probably responsible for the observed defects in replication and repair and support the proposal that the different SSB binding modes may function selectively in replication, recombination and/or repair.

Biopolymers↗
PubMed2005

Asymmetric distribution of cooperativity in the binding cascade of normal human hemoglobin. 2. Stepwise cooperative free energy.

Stepwise cooperative free energies and intermediate Hill coefficients are used to assess the presence of noncooperative sequences in the database of binding free energies previously obtained for the eight partially ligated intermediates of human hemoglobin, encompassing a variety of hemesite analog substitutions. This analysis is prompted by the observed noncooperative binding of two ligands to hemoglobins that are partially substituted with Zn2+-heme, an analog of deoxy Fe2+-heme (Holt et al. (2005) Biochemistry 44, XXXXX). The results show that noncooperative binding sequences are observed in all hemesite analog studied to date. The noncooperative binding observed in (alpha2Znbeta2FeO2) and (alpha2FeO2beta2Zn) is therefore not a Zn-specific substitution artifact. One of several binding sequences from singly to triply ligated hemoglobin is also observed to occur with little or no positive cooperativity. These results demonstrate the variability possible among different ligation pathways in a highly cooperative multi-subunit system such as hemoglobin. As a direct consequence of this variability, differences among ligation pathways are not always detectable using cooperativity functions based on statistical distributions, such as the Hill coefficient n(H). The limitations of Hill coefficient analysis in evaluating cooperativity in intermediates of complex systems is contrasted with the utility of the stepwise binding parameters.

Energy Transfer↗
PubMed1997

Half-site reactivity, negative cooperativity, and positive cooperativity: quantitative considerations of a plausible model.

The nature of cooperative allosteric interactions has been the source of controversy since the ground-breaking studies of oxygen binding to hemoglobin. Until recently, quantitative examples of a model based on the inherent symmetry and asymmetry of oligomeric proteins have been lacking. This laboratory has used the phenolic ligand binding characteristics of the insulin hexamer to develop the first quantitative model for a symmetry-asymmetry-based cooperativity mechanism. The insulin hexamer possesses positive and negative heterotropic and homotropic interactions involving two classes of sites. In this study, we explore the effects of heterotropic interactions between these sites. We show that application of the pairwise structural asymmetry theory of Seydoux, Malhotra, and Bernhard (SMB) gives excellent agreement between the ligand binding behavior and X-ray crystal structure data. Furthermore, by comparing experimental data with computer simulations, we show that the insulin hexamer can be described by a three-state SMB model involving two positive homotropic cooperative transitions linked by a negative homotropic interaction. The first transition, T3T3' right harpoon over left harpoon T3oR3o, with allosteric constant LoA = [T3T3']/[T3oR3o] and ligand dissociation constant KRo consists of a positive cooperative change from high to low symmetry that results in "half-site reactivity". The second transition, T3oR3o right harpoon over left harpoon R3R3', with allosteric constant LoB = [T3oR3o]/[R3R3'] and ligand dissociation constant KR is a change from low to high symmetry, which is also a positive cooperative process. Treatment of the two transitions as concerted and interconnected processes allows derivation of an equation for the fraction of R-state. Using this equation, the effects of changes in the four physical parameters, LoA, LoB, KR, and KRo, on the ligand binding properties of the insulin hexamer are quantitatively described.

Allosteric Regulation↗
PubMed1978

Studies of the chemo-mechanical conversion in artificially produced streamings. III. Dynamic cooperativity--a new cooperativity in actomyosin systems with a polarized arrangement of F-actin.

The order--disorder phase transition in the chemo-mechanical process in our streaming system, which was reported in the preceding paper [Yano, M. & Shimizu, H., J. Biochem, 84, 1087--1092], was studied in detail. Starting from the hypothesis that a new type of cooperativity, dynamic cooperativity, is present in the elementary cycles of the chemo-mechanical conversion, quantitative and consistent agreement was obtained between the theoretical and experimental data on the temperature dependences of the streaming velocity and the ATPase activity, including the presence of the phase transition. The hypothesis was also supported by observations of the temperature dependence of the ATPase activity in resisted streaming. The physical and physiological significance of dynamic cooperativity is considered. It is shown that dynamic cooperativity arises in actomyosin system which have a polarized arrangement of F-actin by directed streaming of the solution, because the rate of the elementary cycle can be accelerated by the streaming. Furthermore, dynamic cooperativity is the key mechanism of self-organization of a dynamical order such that in ordered motions, and is one of the essential conditions for the direct conversion of the chemical energy of ATP to the mechanical energy of ordered and directed motion.

Actins↗
PubMed1982

Lipid-dependent membrane enzymes. A kinetic model for cooperative activation in the absence of cooperativity in lipid binding.

The dependence of integral membrane enzymes on lipid activators in analyzed in terms of multiple binding site kinetics. Rate equations for an enzyme with n independent and indentical lipid binding sites are derived for the case that enzyme activity is proportional to the total amount of lipid bound, or that only fully substituted enzyme is active. A third equation applies to the case that lipids bind with infinite cooperativity to give fully substituted and active enzyme. None of the three models was entirely consistent with existing experimental data. The following kinetic model is shown to accommodate the degree of cooperativity observed in lipid activation experiments as well as the number of independent lipid-binding sites determined by electron-spin resonance measurements. The membrane enzyme is assumed to have n non-interacting and identical lipid-binding sites. Only fully substituted enzyme (ELn) and the next most highly substituted forms such as ELn-1 and ELn-2 may possess enzyme activity. These assumptions lead to cooperativity in activation. Cooperativity reaches a maximum when enzyme activity starts to appear with about 80% of the full lipid substitution. The increase in cooperativity is accompanied by a decrease in the lipid concentration required for half-maximal activation. Further kinetic aspects of a dynamic boundary lipid layer around integral membrane enzymes are discussed.

Allosteric Regulation↗
PubMed1985

Cooperative and non-cooperative processes of apparent movement of random-dot cinematograms.

In this study, we investigated the cooperative and non-cooperative models of stereopsis on apparent movement of the short-range process using spatial frequency filtered random-dot cinematograms. Our results showed that when spatial frequencies were below 4 cycles/degree, maximum displacement (dmax) was decreasing (linearly) with increasing mean frequencies, but at 4 cycles/degree and above dmax stayed constant. For low frequencies, non-cooperative models such as Marr and Poggio's could explain these findings, but not for frequencies above 4 cycles/degree. However, in a previous study we found that the average cooperative neighbourhood for apparent movement of the short-range process is 15 arc min. This fortuitous agreement on 4 cycles/degree could suggest that dmax being constant at frequencies above 4 cycles is related to a cooperative process.

Depth Perception↗
PubMed1977

Cooperativity concepts in protein binding models--problems of cooperativity definition, detection, identification and measuring.

Cooperativity in protein-ligand binding cannot yet be treated as a urinary phenomenon (neither in investigating nor in modelling), although imaginable to rest upon some few general principles only. Knowledge of atomic details of protein-ligand interactions is still limited. Instead of a physico-chemical explanation and definition of cooperativity, a series of schematic concept has been established throughout the literature. Some dominating or merely observable features are isolated and intermixed with plausibly invented mechanistic details. These cooperativity concepts are put together and partly generalized here. From comparing these concepts with the state of binding theory on the one hand and with the nature of measured binding data on the other, some problems of understanding cooperative effects and of detecting, measuring and identifying them are pointed out. For special cases, suitable criteria and measures are recommended and graphic and mathematical techniques discussed. The limited significance and generality of current cooperativity terms is emphasized. Some different levels of understanding have to be distinguished.

Ligands↗
PubMed1985

Cooperative behaviour in monomeric enzymes. Change of negative to positive cooperativity by effect of a ligand.

Three steady-state models were analysed to see if they could reproduce the following kinetic characteristics in a monomeric enzyme with two substrates: a) kinetic cooperativity with respect to the first substrate but not to the second; b) modulation of the kinetic cooperativity for the first substrate by the concentration of the second; c) change in the sign of the kinetic cooperativity at very low concentrations of the second substrate. A slow transition model previously proposed for vertebrate "glucokinase" (hexokinase D), model I, (Olavarría et al., 1982) was able to reproduce characteristics a and b, but never c. The "mnemonical" model (Ricard et al., 1974), model II, also reproduced characteristics a and b, and failed to reproduce c. Thus when observations were performed at concentrations of the first substrate around K0.5 it was possible to observe a decrease in the Hill coefficient (h) relative to the decrease in the concentration of the second substrate, but values lower than 1.0 were never obtained. At extremely high substrate concentrations, the second substrated did not affect the cooperativity of the enzyme for the first substrate. Model III was similar to Model I, but it was considered that only the enzyme conformer with the higher affinity for the first substrate was catalytically active. With this model it was possible to change positive cooperativity into negative if the second substrated altered the frequency of the conformational transition.

Binding Sites↗
PubMed2004

Health cooperation in an hospital of a rural area of Ivory Coast: analysis of the priorities and of the different levels at which cooperation can take place.

This paper critically reviews an experience of health cooperation in an hospital of a rural area of Ivory Coast. This particular situation is analysed in the more general frame of health problems in low-income countries and may suggest priorities for international health cooperation. The analysis of the main causes of avoidable death in poor countries does indicate targets and tools of intervention. In this case, the target was the reduction of infant mortality from anaemia of different origin and from HIV-1 mother-to-infant transmission. The major tool for intervention was the partnership between an Italian teaching and research hospital and the African hospital, with the catalyst of a non-governmental organisation. This paper analyses the different levels at which cooperation developed in this project, from sheer economic support to the implementation of disease-oriented twinning programs that can improve health care and strengthen research capacity on both sides. Besides, medical, ethical and social implications of the ongoing cooperation program are discussed, with particular reference to the problems of preventing mortality from severe anaemia (diet fortification in children and pregnancy and transfusional guidelines in severe malaria) and of preventing mother-to-child neonatal transmission of HIV-1 infection (counselling and testing pregnant women for HIV-1, nevirapine administering to the mother and the baby and breast-feeding).

Adult↗
PubMed2002

Analysing protein energy data by a stochastic model for cooperative interactions: comparison and characterization of cooperativity.

In the frame of a Markov chain model for cooperative interactions in proteins, previously introduced by us, we deal here with estimation of unknown parameters from protein energy data. One of these parameters characterizes the cooperativity of a protein; we propose to measure it also by the so-called approximate entropy. By our computations the approximate entropy turns out to be a decreasing function of the cooperativity. We analyse both simulated data of the Markov chain, and protein energy data obtained by molecular dynamics simulation. Moreover, we compare two rubredoxin proteins at different temperatures, according to their degrees of cooperativity.

Computer Simulation↗
PubMed2006

Cooperative hydrogen bonds of macromolecules. 2. Two-dimensional cooperativity in the binding of poly(4-vinylpyridine) to poly(4-vinylphenol).

The hydrogen bond interaction of poly(4-vinylphenol) (PVF), ligated by a 20 mol/mol excess of pyridine-d(5) (PD) in tetrahydrofuran-d(8), with poly(4-vinylpyridine) (PVP) was studied using liquid and solid-state NMR and quantum mechanical calculations. Because of its cooperative interaction, PVP substitutes PD in its hydrogen bond with PVF, thus forming a PVF-PVP complex, which gradually precipitates from solution. On the basis of the 1H/13C NMR spin-diffusion experiments and density functional theory quantum calculations, the complex is shown to have the fairly regular structure of a polymer sheet with intermittent H-bond links between PVF and PVP chains. The cooperativity of PVP interaction with PVF was studied by measuring the dependence of the binding degree alpha of PVP on its polymerization degree (P(n), being 10, 17, 30, 36, 48, 65, and 84) at various PVP/PVF molar ratios. The value of alpha was established indirectly by measuring the fraction of liberated PD using its 2H quadrupolar relaxation and pulsed field-gradient spin-echo measurement of self-diffusion. The cooperativity is shown to be of a higher order and two-dimensional, that is, dependent on both the polymerization degree of PVP and its ratio to PVF. A mathematical model of such two-dimensional cooperativity based chiefly on a proximity effect is suggested.

Journal Article↗
PubMed2004

Absence of p21WAF1 cooperates with c-myc in bypassing Ras-induced senescence and enhances oncogenic cooperation.

The absence of p21waf1 combined with an ectopic expression of c-myc prevents ras-induced senescence in mouse embryo fibroblasts. Extension of lifespan after c-myc transduction into p21-null cells was followed at later passages by apoptosis of a large fraction of c-myc-overexpressing p21-null cells. This apoptotic effect could be overridden by inactivation of the p53 tumor suppressor or oncogenic ras expression. Ras-induced inhibition of apoptosis is mediated by PI3K activation. These results suggest a functional relationship between ras and myc that may explain their oncogenic cooperation. The number of foci formed by myc+ras increased cooperatively in the absence of p21waf1. Thus, the reciprocal cooperation between myc and ras in a p21-null background during cellular immortalization lead to increased oncogenic cooperation between ras and myc.

Animals↗
PubMed2005

Eliciting survey cooperation: incentives, self-interest, and norms of cooperation.

Given the weaker ties to community as noted by scholars such as Robert Putnam, survey researchers should not be surprised by a decline in survey participation over the past 10 years. This research analyzes the use of incentives coupled with introductory themes emphasizing cooperation and helpfulness--cooperative norms in American society--to understand their effects on survey response. This article analyzes two separate experiments (one phone and one mail) that provide evidence that norms of cooperation matter in the decision to participate in a survey, suggesting that this is particularly true at the refusal conversion stage. These results indicate that survey researchers may use such themes to their advantage, especially when conducting a nonresponse follow-up in a mail survey.

Cooperative Behavior↗
PubMed2004

Hydrogen-bonding cooperativity: using an intramolecular hydrogen bond to design a carbohydrate derivative with a cooperative hydrogen-bond donor centre.

Neighbouring groups can be strategically located to polarise HO.OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO.OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3-cis-diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1-3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule.

Journal Article↗
PubMed2002

Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins.

Potentials of mean force (PMFs) of three-body hydrophobic association are investigated to gain insight into similar processes in protein folding. Free energy landscapes obtained from explicit simulations of three methanes in water are compared with that predicted by popular implicit-solvent effective potentials for the study of proteins. Explicit-water simulations show that for an extended range of three-methane configurations, hydrophobic association at 25 degrees C under atmospheric pressure is mostly anti-cooperative, that is, less favorable than if the interaction free energies were pairwise additive. Effects of free energy nonadditivity on the kinetic path of association and the temperature dependence of additivity are explored by using a three-methane system and simplified chain models. The prevalence of anti-cooperativity under ambient conditions suggests that driving forces other than hydrophobicity also play critical roles in protein thermodynamic cooperativity. We evaluate the effectiveness of several implicit-solvent potentials in mimicking explicit water simulated three-body PMFs. The favorability of the contact free energy minimum is found to be drastically overestimated by solvent accessible surface area (SASA). Both the SASA and a volume-based Gaussian solvent exclusion model fail to predict the desolvation barrier. However, this barrier is qualitatively captured by the molecular surface area model and a recent "hydrophobic force field." None of the implicit-solvent models tested are accurate for the entire range of three-methane configurations and several other thermodynamic signatures considered.

Animals↗
PubMed1997

Cooperative and non-cooperative DNA binding modes of catabolite control protein CcpA from Bacillus megaterium result from sensing two different signals.

Carbon catabolite repression (CCR) of several operons in Bacillus subtilis and Bacillus megaterium is mediated by the cis-acting cre sequence and trans-acting catabolite control protein (CcpA). We describe purification of CcpA from B. megaterium and its interaction with regulatory sequences from the xyl operon. Specific interaction of CcpA with cre as scored by DNase I footprints at concentrations similar to the in vivo situation requires the presence of effectors. We have found two molecular effectors for CcpA activity, which lead to different recognition modes of DNA. The heat-stable phosphotransfer protein HPr from the PTS sugar uptake system triggers non-cooperative binding of CcpA to cre when phosphorylated at Ser46 (HPr-Ser46-P). Glucose 6-phosphate (Glc-6-P) triggers cooperative binding of CcpA to cre and two auxiliary cre* sites, one of which overlaps the -35 box of the xyl promoter. Binding to cre* depends on the presence of the functional cre sequence. A mutation in cre abolishes carbon catabolite repression in vivo and binding of CcpA to cre and cre* in vitro, indicating looping of the intervening DNA. The two triggers are not simultaneously active. The acidity of the buffer determines which of them activates CcpA when both are present in vitro. Glc-6-P is preferred at pH values below 5.4, and HPr-Ser46-P is preferred at neutral pH. The Ccpa dimers present at neutral pH form tetramers and higher oligomers at pH 4.6, explaining cooperativity of binding to DNA. CcpA is the first member of the LacI/GalR family of regulators, for which oligomerization without the leucine zipper at the C terminus is demonstrated.

Bacillus megaterium↗
PubMed1983

Cooperative lipid activation of (Na+ + K+)-ATPASE as a consequence of non-cooperative lipid-protein interactions.

Lipid activation data for (Na+ + K+)-ATPase (Ottolenghi, P. (1979) Eur. J. Biochem. 99, 113-131) have been subjected to a regression and fitting analysis based on a recent kinetic model (Sandermann, H. (1982) Eur. J. Biochem, 127, 123-128). The observed kinetic cooperativity could be generated from strictly non-cooperative binding events involving the known number of 30 boundary lipid-binding sites per ATPase monomer. Apparent lipid dissociation equilibrium constants of between 0.3 and 5 microM were obtained, enzyme activity being associated only with the fully lipid-substituted enzyme and enzyme-lipid complexes with less than six unoccupied lipid-binding sites. The enzyme appeared to operate close to a maximum of cooperativity.

Animals↗
PubMed1978

Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions.

A combinatorial approach is employed to calculate exact expressions for the extent of binding to a finite one dimensional lattice of ligands which cover more than one lattice site. The binding may be either cooperative or non-cooperative. It is found that the assumption of an effectively infinite lattice is generally a good one, except with relatively low concentrations of strongly cooperative ligands. An approach to analyzing experimental data is suggested which makes explicit use of the lattice length dependence of binding to extract more information about the binding parameters than can be obtained using the infinite lattice approximation. It is shown that irreversible binding cannot be viewed as a limiting case of reversible binding. The reasons for this difference are discussed, and expressions for the extent of irreversible binding are derived.

Binding Sites↗