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Results for “Solvent accessibility”

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PubMed1994

Peptide-induced conformational changes in class I molecules. Direct detection by flow cytometry.

Activation of a T cell in response to peptide bound to class I MHC occurs by the sum of interactions across the area of contact between the TCR, the peptide, and class I MHC. It has been observed recently that substitution of the peptide residue at a position that is not accessible from the exterior of the class I molecule modulates T cell responses, raising the possibility that there may be indirect structural effects in the peptide-class I complex as a consequence of peptide binding. This report describes the use of mAbs to probe the conformation of the alpha 1 and alpha 2 domains of the mouse class I molecule Kb when bound to ovalbumin peptide and a panel of 19 peptide analogues that differ at position 2 (P2). By crystallographic data, side chains of this position are buried in the Ag binding cleft and have no direct access to the TCR. Substitution of position 2 results in a measurable change in conformation of the class I molecule, a change that correlates with the ability to stimulate T cells. This leads to a model that T cell activation by the peptide-class I complex may occur in three ways: 1) direct interaction of the TCR with the class I heavy chain, 2) direct interaction of the TCR with solvent-accessible peptide side chains, and 3) indirect interaction of peptide with TCR mediated via conformational perturbations in the class I complex.

Amino Acid Sequence↗

PubMed1988

Fluorescence quenching studies of fluorescein attached to Lys-61 or Cys-374 in actin: effects of polymerization, myosin subfragment-1 binding, and tropomyosin-troponin binding.

The resonance energy transfer between fluorescein-5-isothiocyanate (FITC) attached to Lys-61 and Co2+ bound to the high-affinity metal binding site was measured. The distance between FITC and Co2+ on the actin molecule was calculated to be either 1.9 nm, using the absorption spectrum of Co-EDTA or 2.8 nm, using the absorption spectrum of Co2+ bound to carboxypeptidase as a model spectrum of Co2+ bound to actin, respectively. The effects of the polymerization of actin and of the interaction of actin with myosin subfragment-1 (S1) on the solvent accessibility of the fluorescein molecule attached to Lys-61 or Cys-374 were measured. The accessibility of the probe at Lys-61 was reduced following polymerization and also appreciably reduced by interaction with S1. The accessibility of the probe attached to Cys-374 was affected to only a small degree. These results indicate that the Lys-61 residue is located close to an actin-actin contact region as well as being close to an S1 binding site, although it is not directly involved [Miki, M. (1987) Eur. J. Biochem. 164, 228-235]. The accessibility of the probe at Lys-61 was also decreased by the addition of the tropomyosintroponin complex, although the accessibility of the probe at Cys-374 was not affected at all. Thus, Lys-61 appears to be involved in the binding site of the regulatory proteins.

Actins↗

PubMed1995

Empirical correlation for the replacement of Ala by Gly: importance of amino acid secondary intrinsic propensities.

A series of Ala vs. Gly mutations at different helical and nonhelical positions of the chemotactic protein CheY, from E. coli, has been made. We have used this information to fit a general analytical equation that describes the free energy changes of an Ala to Gly mutation within +/- 0.45 kcal mol-1 with 95% confidence. The equation includes three terms: (1) the change in solvent-accessible hydrophobic surface area, corrected for the possible closure of the cavity left by deleting the C beta of the Ala; (2) the change in hydrophilic area of the nonintramolecularly hydrogen-bonded groups; and (3) the dihedral angles of the position being mutated. This last term extends the calculation to any conformation, not only alpha-helices. The general applicability of the equation for Ala vs. Gly mutations, when Ala or a small solvent-exposed polar residue is the wild-type residue, has been tested using data from other proteins: barnase, CI2 trypsin inhibitor, T4 lysozyme, and Staphylococcus nuclease. The predictive power of this simple approach offers the possibility of extending it to more complex mutations.

Alanine↗

PubMed1998

Apomyoglobin folding intermediates characterized by the hydrophobic fluorescent probe 8-anilino-1-naphthalene sulfonate.

Folding apomyoglobin intermediates were investigated by optical techniques including steady-state fluorescence, frequency domain fluorometry, and absorption spectroscopy. The investigated chromophores were the aromatic residues, i.e., tyrosyl and tryptophanyl residues, and the extrinsic probe (8-anilino-1-naphthalenesulfonate, ANS) which is particularly useful for studying partly structured forms appearing in the early stage of protein folding. The emission decay of the extrinsic probe as well as resonance energy transfer from tryptophanyl residues to ANS permitted to identify and characterize partly folded forms obtained under different experimental conditions. The results indicate that the intermediates so far detected (I-1 and I-2 states) are distinct structural states. The differences concern the solvent accessibility to the aromatic side chains and the conformational dynamics of the protein region forming the binding site for the extrinsic fluorophore.

Anilino Naphthalenesulfonates↗

PubMed2004

Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.

Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with the generalized Born continuum dielectric model, energies calculated by the 10(6)-fold slower finite difference Poisson-Boltzmann model are faithfully reproduced. A similar approach can be used for estimating solvent-accessible surface areas (SASAs). As an independent test, we show that these approximations can be used to accurately predict the experimentally determined pK(a)s of >200 ionizable groups from 15 proteins.

Algorithms↗

PubMed2006

Redox properties of the Fe3+/Fe2+ couple in Arthromyces ramosus class II peroxidase and its cyanide adduct.

The thermodynamics of the one-electron reduction of the ferric heme in free and cyanide-bound Arthromyces ramosus peroxidase (ARP), a class II plant peroxidase, were determined through spectro-electrochemical experiments. The data were compared with those for class III horseradish peroxidase C (HRP) and its cyanide adduct, and were interpreted in terms of ligand binding features, electrostatic effects and solvent accessible surface area of the heme group and of catalytically relevant residues in the heme distal site. The E(o)' values for free and cyanide-bound ARP (-0.183 and -0.390 V, respectively, at 25 degrees C and pH 7) are higher than those for HRP and HRP-CN. ARP features an enthalpic stabilization of the ferrous state and a remarkably negative reduction entropy, which are both unprecedented for heme peroxidases. Once the compensatory contributions of solvent reorganization are partitioned from the measured reduction enthalpy, the resulting protein-based deltaH(o)'(rc(int)) value for ARP turns out to be less positive than that for HRP by +10 kJ mol(-1). The smaller stabilization of the oxidized heme in ARP most probably results from the less pronounced anionic character of the proximal histidine, and the decreased polarity in the heme distal site as compared with HRP, as indicated by the X-ray structures. The surprisingly negative deltaS(o)'(rc) value for ARP is the result of peculiar reduction-induced solvent reorganization effects.

Crystallography, X-Ray↗

PubMed2006

Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins.

The environmental preference for the occurrence of noncanonical hydrogen bonding and cation-pi interactions, in a data set containing 71 nonredundant (alpha/beta)(8) barrel proteins, with respect to amino acid type, secondary structure, solvent accessibility, and stabilizing residues has been performed. Our analysis reveals some important findings, which include (a) higher contribution of weak interactions mediated by main-chain atoms irrespective of the amino acids involved; (b) domination of the aromatic amino acids among interactions involving side-chain atoms; (c) involvement of strands as the principal secondary structural unit, accommodating cross strand ion pair interaction and clustering of aromatic amino acid residues; (d) significant contribution to weak interactions occur in the solvent exposed areas of the protein; (e) majority of the interactions involve long-range contacts; (f) the preference of Arg is higher than Lys to form cation-pi interaction; and (g) probability of theoretically predicted stabilizing amino acid residues involved in weak interaction is higher for polar amino acids such as Trp, Glu, and Gln. On the whole, the present study reveals that the weak interactions contribute to the global stability of (alpha/beta)(8) TIM-barrel proteins in an environment-specific manner, which can possibly be exploited for protein engineering applications.

Amino Acids↗

PubMed2005

Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation.

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.

Journal Article↗

PubMed1998

Stability effects of increasing the hydrophobicity of solvent-exposed side chains in staphylococcal nuclease.

A total of fifty single site surface phenylalanine substitution mutants have been made in the model protein staphylococcal nuclease. The fifty residues that were replaced with phenylalanine were chosen to give a broad sampling of solvent accessibility, secondary structure, and backbone conformations. The change in the stability of each mutant protein relative to wild type was measured by guanidine hydrochloride denaturation. These results were compared to previous results obtained when these same sites were substituted with an alanine and a glycine. By this means, changes in the stability due to the loss of interactions of the wild-type side chain can be separated from the effects of introducing the bulky, hydrophobic phenylalanine in these solvent-exposed positions. In general, our results agree with the conventional wisdom that placing a hydrophobic residue in a solvent-exposed position is destabilizing in most cases, but less destabilizing than most changes in the hydrophobic core of the protein. However, the degree to which a hydrophobic surface substitution destabilizes or stabilizes a globular protein is highly context-dependent, with some mutations being as destabilizing as those in the core. This indicates that steric and packing considerations are also important on the surface of a globular protein but generally are not as important as in the interior. No evidence for the widespread occurrence of the so-called reverse hydrophobic effect at solvent-exposed sites was found. In addition, this survey of numerous sites suggests that previous measurements of alpha-helix "propensities" often seriously underestimate the importance of the environment of the side chain.

Amino Acid Sequence↗

PubMed2003

Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer.

The present study tests performance of different solvation models applied to molecular dynamics simulation of a large, dimeric protein molecule. Analytical Continuum Electrostatics (ACE) with two different parameter sets, older V98 and new V01, and Effective Energy Function (EEF) are employed in molecular dynamics simulation of immunoglobulin G (IgG) light chain dimer and variable domain of IgG light chain. Results are compared with explicit solvent and distance dependent dielectric constant (DDE) calculations. The overall analysis shows that the EEF method yields results comparable to explicit solvent simulations; however, the stability of simulations is lower. On the other hand, the ACE_V98 model does not seem to achieve the accuracy or stability expected in nanosecond timescale MD simulation for the studied systems. The ACE_V01 model greatly improves stability of the calculation; nonetheless, changes in radius of gyration and solvent accessible surface of the studied systems may indicate that the parameter set still needs to be improved if the method is supposed to be used for simulations of large, polymeric proteins. Additionally, electrostatic contribution to the solvation free energy calculated in the ACE model is compared with a numerical treatment of the dielectric continuum model. Wall clock time of all simulations is compared. It shows that EEF calculation is six times faster than corresponding ACE and 50 times faster than explicit solvent simulations.

Computer Simulation↗

PubMed2000

Free energy landscapes of peptides by enhanced conformational sampling.

The free energy landscapes of peptide conformations in water have been observed by the enhanced conformational sampling method, applying the selectively enhanced multicanonical molecular dynamics simulations. The conformations of the peptide dimers, -Gly-Gly-, -Gly-Ala-, -Gly-Ser-, -Ala-Gly-, -Asn-Gly-, -Pro-Gly-, -Pro-Ala-, and -Ala-Ala-, which were all blocked with N-terminal acetyl and C-terminal N-methyl groups, were individually sampled with the explicit TIP3P water molecules. From each simulation trajectory, we obtained the canonical ensemble at 300 K, from which the individual three-dimensional landscape was drawn by the potential of mean force using the three reaction coordinates: the backbone dihedral angle, psi, of the first amino acid, the backbone dihedral angle, phi, of the second amino acid, and the distance between the carbonyl oxygen of the N-terminal acetyl group and the C-terminal amide proton. The most stable state and several meta-stable states correspond to extended conformations and typical beta-turn conformations, and their free energy values were accounted for from the potentials of mean force at the states. In addition, the contributions from the intra-molecular energies of peptides and those from the hydration effects were analyzed. Consequently, the stable beta-turn conformations in the free energy landscape were consistent with the empirically preferred beta-turn types for each amino acid sequence. The thermodynamic values for the hydration effect were decomposed and they correlated well with the empirical values estimated from the solvent accessible surface area of each molecular conformation during the trajectories. The origin of the architecture of protein local fragments was analyzed from the viewpoint of the free energy and its decomposed factors.

Algorithms↗

PubMed2003

Protocol for MM/PBSA molecular dynamics simulations of proteins.

Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations.

Computer Simulation↗

PubMed2006

Transmembrane segment 12 of the Glut1 glucose transporter is an outer helix and is not directly involved in the transport mechanism.

A model has been proposed for the exofacial configuration of the Glut1 glucose transporter in which eight transmembrane domains form an inner helical bundle stabilized by four outer helices. The role of transmembrane segment 12, predicted to be an outer helix in this hypothetical model, was examined by cysteine-scanning mutagenesis and the substituted cysteine accessibility method using the membrane-impermeant, sulfhydryl-specific reagent, p-chloromercuribenzenesulfonate (pCMBS). A previously characterized functional cysteine-less Glut1 molecule was used to produce 21 Glut1 point mutants by changing each residue along helix 12 to a cysteine residue. These mutants were then expressed in Xenopus oocytes, and their protein levels, functional activities, and sensitivities to pCMBS were determined. Strikingly, in contrast to all nine other predicted Glut1 transmembrane helices that have been previously examined by this method, none of the 21 helix 12 single-cysteine mutants exhibited significant inhibition of specific transport activity. Also unlike most other Glut1 transmembrane domains in which solvent-accessible residues lie along a single face of the helix, mutations in five consecutive residues predicted to lie close to the exofacial face of the membrane resulted in sensitivity to pCMBS-induced transport inhibition. These results suggest that helix 12 plays a passive stabilizing role in the structure of Glut1 and is not directly involved in the transport mechanism. Additionally, the pCMBS data indicate that the predicted exoplasmic end of helix 12 is completely exposed to the external solvent when the transporter is in its exofacial configuration.

4-Chloromercuribenzenesulfonate↗

PubMed2005

Accessibility and dynamics of nitroxide side chains in T4 lysozyme measured by saturation recovery EPR.

Long pulse saturation recovery electron paramagnetic resonance spectroscopy is applied to the investigation of spin-labeled side chains placed along a regular helix extending from 128 to 135 in T4 lysozyme. Under an argon atmosphere, analysis of the exponential saturation recovery curves gives the spin-lattice relaxation rates of the nitroxides, which depend on the nitroxide side-chain dynamics. In the presence of the fast-relaxing paramagnetic reagents O(2) or NiEDDA, global analysis of the saturation recovery provides the spin-lattice relaxation rates as well as the Heisenberg exchange rates of the nitroxide with the reagents. As previously shown with power saturation methods, such exchange rates are direct measures of the solvent accessibility of the nitroxide side chains in the protein structure. The periodic dependence of the spin-lattice relaxation rates and the exchange rates along the 128-135 sequence reveal the presence of the helical structure, demonstrating the use of these parameters in structure determination. In general, multiple exponentials are required to fit the saturation recovery data, thus identifying multiple states of the side chain. In one case, multiple conformations detected in the spectrum are not evident in the saturation recovery, suggesting rapid exchange on the timescale of spin-lattice relaxation.

Argon↗

PubMed2000

Tryptophan fluorescence of calmodulin binding domain peptides interacting with calmodulin containing unnatural methionine analogues.

The interactions between the abundant methionine residues of the calcium regulatory protein calmodulin (CaM) and several of its binding targets were probed using fluorescence spectroscopy. Tryptophan steady-state fluorescence from peptides encompassing the CaM-binding domains of the target proteins myosin light chain kinase (MLCK), cyclic nucleotide phosphodiesterase (PDE) and caldesmon site A and B (CaD A, CaD B), and the model peptide melittin showed Ca(2+)-dependent blue-shifts in their maximum emission wavelength when complexed with wild-type CaM. Blue-shifts were also observed for complexes in which the CaM methionine residues were replaced by selenomethionine, norleucine and ethionine, and when a quadruple methionine to leucine C-terminal mutant of CaM was studied. Quenching of the tryptophan fluorescence intensity was observed with selenomethionine, but not with norleucine or ethionine substituted protein. Fluorescence quenching studies with added potassium iodide (KI) demonstrate that the non-native proteins limit the solvent accessibility of the Trp in the MLCK peptide to levels close to that of the wild-type CaM-MLCK interaction. Our results show that the methionine residues from CaM are highly sensitive to the target peptide in question, confirming the importance of their role in binding interactions. In addition, we provide evidence that the nature of binding in the CaM-CaD B complex is unique compared with the other complexes studied, as the Trp residue of this peptide remains partially solvent exposed upon binding to CaM.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed1997

Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting.

To clarify further the mechanism of regulation by phosphorylation of isocitrate dehydrogenase, cocrystallization of isocitrate dehydrogenase and isocitrate dehydrogenase kinase/phosphatase in the presence of an ATP analog was attempted. Although cocrystallization was unsuccessful, a new crystal form of isocitrate dehydrogenase was obtained which provides insight into the phosphorylation mechanism. The new, orthorhombic crystal form of isocitrate dehydrogenase is related to the previously reported tetragonal form largely by an approximately 16 degrees shift of a large domain relative to the small domain and clasp region within each subunit of the dimeric enzyme. The NADP+ cofactor binding surface is significantly disrupted by the shift to the open conformation. The solvent-accessible surface area and surface-enclosed volume increase by 2% relative to the dimeric tetragonal form. Most of the increase results from expansion of the active site cleft such that the distance across its opening increases from approximately 5 to 13 A, significantly increasing accessibility to Ser-113. The conformation of isocitrate dehydrogenase in the orthorhombic crystal form more closely resembles that of the crystal structure of the homologous enzyme 3-isopropylmalate dehydrogenase than does the tetragonal isocitrate dehydrogenase conformation. Since the crystal lattice forces are fairly weak, it appears that isocitrate dehydrogenase is a flexible molecule that can easily undergo domain shifts and possibly other induced fit conformational changes, to accommodate binding to isocitrate dehydrogenase kinase/phosphatase.

Binding Sites↗

PubMed1996

Bridging the protein sequence-structure gap by structure predictions.

The problem of accurately predicting protein three-dimensional structure from sequence has yet to be solved. Recently, several new and promising methods that work in one, two, or three dimensions have invigorated the field. Modeling by homology can yield fairly accurate three-dimensional structures for approximately 25% of the currently known protein sequences. Techniques for cooperatively fitting sequences into known three-dimensional folds, called threading methods, can increase this rate by detecting very remote homologies in favorable cases. Prediction of protein structure in two dimensions, i.e. prediction of interresidue contacts, is in its infancy. Prediction tools that work in one dimension are both mature and generally applicable; they predict secondary structure, residue solvent accessibility, and the location of transmembrane helices with reasonable accuracy. These and other prediction methods have gained immensely from the rapid increase of information in publicly accessible databases. Growing databases will lead to further improvements of prediction methods and, thus, to narrowing the gap between the number of known protein sequences and known protein structures.

Amino Acid Sequence↗

PubMed1998

The solvent-protected core of the hairpin ribozyme-substrate complex.

The complex between the hairpin ribozyme and its substrate consists of two domains that must interact in order to form a catalytic complex, yet experimental evidence concerning the points of interaction between the two domains has been lacking. Here, we report the use of hydroxyl radical footprinting to define the interface between the two domains. Cations that support very efficient ribozyme catalysis (magnesium and cobalt(III) hexammine) lead to the formation of a docked complex that features several regions of protection, indicating a solvent-inaccessible core within the tertiary structure of the complex. Cations that are suboptimal in cleavage reactions do not produce complexes with regions of reduced solvent accessibility. Nucleotides encompassing the substrate cleavage site (c-2, a-1, g+1, and u+2) are strongly protected, suggesting their internalization into the catalytic core. Four distinct segments of the ribozyme are protected, including G11-A14, C25-C27, A38, and U42-A43. Protection of these sites is eliminated when g+1, an essential base at the cleavage site, is replaced by A. In addition, mutations which are known to decrease the fraction of docked complexes decrease or eliminate formation of a solvent-inaccessible core. Taken together, these observations demonstrate that we have identified the catalytic core of the active hairpin ribozyme-substrate complex.

Base Sequence↗