SEARCH · PubMed Health

Results for “Solvent accessibility”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources

PubMed2002

Modeling the structure of agitoxin in complex with the Shaker K+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles.

Computational methods are used to determine the three-dimensional structure of the Agitoxin (AgTx2)-Shaker complex. In a first stage, a large number of models of the complex are generated using high temperature molecular dynamics, accounting for side chain flexibility with distance restraints deduced from thermodynamic analysis of double mutant cycles. Four plausible binding mode candidates are found using this procedure. In a second stage, the quality and validity of the resulting complexes is assessed by examining the stability of the binding modes during molecular dynamics simulations with explicit water molecules and by calculating the binding free energies of mutant proteins using a continuum solvent representation and comparing with experimental data. The docking protocol and the continuum solvent model are validated using the Barstar-Barnase and the lysozyme-antibody D1.2 complexes, for which there are high-resolution structures as well as double mutant data. This combination of computational methods permits the identification of two possible structural models of AgTx2 in complex with the Shaker K+ channel, additional structural analysis providing further evidence in favor of a single model. In this final complex, the toxin is bound to the extracellular entrance of the channel along the pore axis via a combination of hydrophobic, hydrogen bonding, and electrostatic interactions. The magnitude of the buried solvent accessible area corresponding to the protein-protein contact is on the order of 1000 A with roughly similar contributions from each of the four subunits. Some side chains of the toxin adopt different conformation than in the experimental solution structure, indicating the importance of an induced-fit upon the formation of the complex. In particular, the side chain of Lys-27, a residue highly conserved among scorpion toxins, points deep into the pore with its positively charge amino group positioned at the outer binding site for K+. Specific site-directed mutagenesis experiments are suggested to verify and confirm the structure of the toxin-channel complex.

Animals↗

PubMed2002

Conformation of a trimannoside bound to mannose-binding protein by nuclear magnetic resonance and molecular dynamics simulations.

A model of the carbohydrate recognition domain of the serum form of mannose-binding protein (MBP) from rat complexed with methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside is presented. Allowed conformations for the bound sugar were derived from simulated annealing protocols incorporating distance restraints computed from transferred NOESY spectra. The resulting sugar conformations were then modeled into the MBP binding site, and these models of the complex were refined using molecular dynamics (MD) simulations in the presence of solvent water. These studies indicate that only one of the two major conformations of the alpha(1-->6) linkage found in solution is significantly populated in the bound state (omega = 60 degrees ), whereas the alpha(1-->3) linkage samples at least two states, similar to its behavior in free solution. The bound conformation allows direct hydrogen bonds to form between the sugar and K182 of MBP, in addition to other water-mediated hydrogen bonds. Estimates of binding constants of candidate complexes based on changes in solvent-accessible surface areas upon binding support the NMR and MD results. These estimates further suggest that the enthalpic gains of the additional sugar-MBP interactions in a trisaccharide as opposed to a monosaccharide are offset by entropic penalties, offering an explanation for previous binding data.

Animals↗

PubMed2003

Stability of the I-motif structure is related to the interactions between phosphodiester backbones.

The i-motif DNA tetrameric structure is formed of two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. The four phosphodiester backbones forming the structure define two narrow and wide grooves. The short interphosphate distances across the narrow groove induce a strong repulsion which should destabilize the tetramer. To investigate this point, molecular dynamics simulations were run on the [d(C2)]4 and [d(C4)]4 tetramers in 3'E and 5'E topologies, for which the interaction of the phosphodiester backbones through the narrow groove is different. The analysis of the simulations, using the Molecular Mechanics Generalized Born Solvation Area and Molecular Mechanics Poisson-Boltzmann Solvation Area approaches, shows that it is the van der Waals energy contribution which displays the largest relative difference between the two topologies. The comparison of the solvent-accessible area of each topology reveals that the sugar-sugar interactions account for the greater stability of the 3'E topology. This stresses the importance of the sugar-sugar contacts across the narrow groove which, enforcing the optimal backbone twisting, are essential to the base stacking and the i-motif stability. Tighter interactions between the sugars are observed in the case of N-type sugar puckers.

Binding Sites↗

PubMed1991

Fluorescence measurements of immune complexes of Mab 4-4-20 with isomeric haptens.

Relative differences in the active site environment of a monoclonal antibody when covalently bound to two isomeric haptens were studied using fluorescence quenching and lifetime measurements. Murine monoclonal antibody 4-4-20, a well-characterized high affinity antifluorescein antibody, served as the model IgG protein. Isomeric haptenic probes comparatively studied were fluorescein-5-isothiocyanate (FITC I, the immunogen) and fluorescein-6-isothiocyanate (FITC II). In kinetic binding studies, the association rate for the interaction of 4-4-20 with FITC I was greater than 2,000 times faster than the reaction with FITC II. Fluorescence lifetimes for FITC I covalently bound to 4-4-20 were 3.89 ns and 0.37 ns, indicative of hapten bound outside and inside the active site, respectively. Fluorescence lifetime for FITC II within the active site was indistinguishable from bound FITC I, indicating that interactions with active site residues which resulted in a decreased lifetime were similar for both isomers. A decreased lifetime for active site bound FITC I was consistent with the 90-95% quenching of fluorescein fluorescence. Dynamic fluorescence quenching experiments with iodide and FITC I in the active site showed no solvent accessibility, whereas bound FITC II showed significant accessibility. These results suggest that the difference in bond angle which accompanies binding of isomer II relative to isomer I within the active site probably leads to steric constraints resulting in a more open configuration of the 4-4-20 active site.

Affinity Labels↗

PubMed1992

Self similarity of protein surfaces.

Scaling properties of the surfaces of 53 proteins are studied on the basis of experimentally determined 3-D structures of these biological macromolecules. It is found that the surfaces show self similarity within a yardstick range of 1.5 A less than epsilon less than 15 A. The self similarity is measured by the fractal dimension D of the surface. Two different algorithms for the determination of the fractal dimension are applied, both based on cubic yardstick particles. One is related to the contact surface (CS), which was first introduced by Connolly (17), while the other corresponds to the solvent accessible surface (SAS) of Richards (9). The fractal dimensions of both are different. While the CS type approach leads to relatively high values of D in the range 2.5 to 2.6 the SAS approach gives fractal dimensions of D approximately 2.

Algorithms↗

PubMed1994

A study of the molecular sources of nonideal osmotic pressure of bovine serum albumin solutions as a function of pH.

The nonideal osmotic pressure of bovine serum albumin (BSA) solutions was studied extensively by Scatchard and colleagues. The extent of pH- and salt-dependent nonideality changes are large and unexplained. In 1992, Fullerton et al. derived new empirical expressions to describe solution nonideal colligative properties including osmotic pressure (Fullerton et al. 1992. Biochem. Cell Biol. 70:1325-1331). These expressions are based on the concepts of volume occupancy and hydration force. Nonideality is accurately described by a solute/solvent interaction parameter I and an "effective" osmotic molecular weight Ae. This paper uses the interaction-corrected nonideal expressions for osmotic pressure to calculate the hydration I values and "effective" osmotic molecular weight of BSA, Ae, as a function of pH. Both factors vary in a predictable manner due to denaturing of the BSA molecule. Both contribute to an increase in osmotic pressure for the same protein concentration as the solution pH moves away from the isoelectric point. Increased nonideality is caused by larger hydration resulting from larger solvent-accessible surface areas and by the decrease in "effective" osmotic molecular weight, Ae, due to segmental motion of denatured (filamentous) molecules.

Hydrogen-Ion Concentration↗

PubMed1994

Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques.

There is a growing body of low-resolution structural data that can be utilized to devise structural models for large RNAs and ribonucleoproteins. These models are routinely built manually. We introduce an automated refinement protocol to utilize such data for building low-resolution three-dimensional models using the tools of molecular mechanics. In addition to specifying the positions of each nucleotide, the protocol provides quantitative estimates of the uncertainties in those positions, i.e., the resolution of the model. In typical applications, the resolution of the models is about 10-20 A. Our method uses reduced representations and allows us to refine three-dimensional structures of systems as big as the 16S and 23S ribosomal RNAs, which are about one to two orders of magnitude larger than nucleic acids that can be examined by traditional all-atom modeling methods. Nonatomic resolution structural data--secondary structure, chemical cross-links, chemical and enzymatic footprinting patterns, protein positions, solvent accessibility, and so on--are combined with known motifs in RNA structure to predict low-resolution models of large RNAs. These structural constraints are imposed on the RNA chain using molecular mechanics-type potential functions with parameters based on the quality of experimental data. Surface potential functions are used to incorporate shape and positional data from electron microscopy image reconstruction experiments into our models. The structures are optimized using techniques of energy refinement to get RNA folding patterns. In addition to providing a consensus model, the method finds the range of models consistent with the data, which allows quantitative evaluation of the resolution of the model. The method also identifies conflicts in the experimental data. Although our protocol is aimed at much larger RNAs, we illustrate these techniques using the tRNA structure as an example and test-bed.

Anticodon↗

PubMed1995

Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates.

The free energy of the stacking-unstacking process of deoxyribodinucleoside monophosphates in aqueous solution has been investigated by potential of mean force calculations along a reaction coordinate, defined by the distance between the glycosidic nitrogen atoms of the bases. The stacking-unstacking process of a ribodinucleoside monophosphate was observed to be well characterized by this coordinate, which has the advantage that it allows for a dynamical backbone and flexible bases. All 16 naturally occurring DNA dimers composed of the adenine, cytosine, guanine, or thymine bases in both the 5' and the 3' positions were studied. From the free-energy profiles we observed the deepest minima for the stacked states of the purine-purine dimers, but good stacking was also observed for the purine-pyrimidine and pyrimidine-purine dimers. Substantial stacking ability was found for the dimers composed of a thymine base and a purine base and also for the deoxythymidylyl-3',5'-deoxythymidine dimer. Very poor stacking was observed for the dCpdC dimer. Conformational properties and solvent accessibility are discussed for the stacked and unstacked dimers. The potential of mean force profiles of the stacking-unstacking process for the DNA dimers are compared with the RNA dimers.

DNA↗

PubMed1997

Electrostatic interactions between transmembrane segments mediate folding of Shaker K+ channel subunits.

In voltage-dependent Shaker K+ channels, charged residues E293 in transmembrane segment S2 and R365, R368, and R371 in S4 contribute significantly to the gating charge movement that accompanies activation. Using an intragenic suppression strategy, we have now probed for structural interaction between transmembrane segments S2, S3, and S4 in Shaker channels. Charge reversal mutations of E283 in S2 and K374 in S4 disrupt maturation of the protein. Maturation was specifically and efficiently rescued by second-site charge reversal mutations, indicating that electrostatic interactions exist between E283 in S2 and R368 and R371 in S4, and between K374 in S4 and E293 in S2 and D316 in S3. Rescued subunits were incorporated into functional channels, demonstrating that a native structure was restored. Our data indicate that K374 interacts with E293 and D316 within the same subunit. These electrostatic interactions mediate the proper folding of the protein and are likely to persist in the native structure. Our results raise the possibility that the S4 segment is tilted relative to S2 and S3 in the voltage-sensing domain of Shaker channels. Such an arrangement might provide solvent access to voltage-sensing residues, which we find to be highly tolerant of mutations.

Animals↗

PubMed1998

Transmembrane helix stability: the effect of helix-helix interactions studied by Fourier transform infrared spectroscopy.

We have measured, using infrared spectroscopy, the hydrogen/deuterium exchange rates of the amide protons in the photosynthetic antenna of Rhodospirillum rubrum. These measurements were made not only on the intact protein in detergent solution but also on two dissociated forms (B820 and B777). We have, on the basis of our knowledge of the structure of this protein, been able to assign the various groups of amide protons that exchange with different time constants to distinct regions of the protein. The most protected group of protons that we observe exchanging with time constants near 6000 min we assign to the transmembrane helices. The slow exchange rates measured for the amide protons of the transmembrane helices of this protein in detergent solution may indicate a destabilization of the helices in detergent solution compared with the membrane. This group of protons is progressively destabilized by stepwise dissociation of the antenna protein, and this destabilization is greater than we can account for by increases in solvent accessibility. We suggest that the observed loss of amide proton protection in the transmembrane helices as they are dissociated might be due to an increase in the helix flexibility and breathing motions as interactions between helices are reduced.

Bacterial Chromatophores↗

PubMed1998

Electrostatic contributions to heat capacity changes of DNA-ligand binding.

Significant heat capacity changes (DeltaCp) often accompany protein unfolding, protein binding, and specific DNA-ligand binding reactions. Such changes are widely used to analyze contributions arising from hydrophobic and polar hydration. Current models relate the magnitude of DeltaCp to the solvent accessible surface area (ASA) of the molecule. However, for many binding systems-particularly those involving non-peptide ligands-these models predict a DeltaCp that is significantly different from the experimentally measured value. Electrostatic interactions provide a potential source of heat capacity changes and do not scale with ASA. Using finite-difference Poisson-Boltzmann methods (FDPB), we have determined the contribution of electrostatics to the DeltaCp associated with binding for DNA binding reactions involving the ligands DAPI, netropsin, lexitropsin, and the lambda repressor binding domain.

Antineoplastic Agents↗

PubMed1998

Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm.

Antifreeze proteins (AFPs) adsorb to surfaces of growing ice crystals, thereby arresting their growth. The prevailing hypothesis explains the nature of adsorption in terms of a match between the hydrophilic side chains on the AFP's ice-binding surface (IBS) and the water molecules on the ice surface. The number and spatial arrangement of hydrogen bonds thus formed have been proposed to account, respectively, for the binding affinity and specificity. The crystal structure of a type III AFP from ocean pout (isoform HPLC-3) has been determined to 2.0-A resolution. The structure reveals an internal dyad motif formed by two 19-residue, loop-shaped elements. Based on of the flatness observed on the type I alpha-helical AFP's IBS, an automated algorithm was developed to analyze the surface planarity of the globular type III AFP and was used to identify the IBS on this protein. The surface with the highest flatness score is formed by one loop of the dyad motif and is identical to the IBS deduced from earlier mutagenesis studies. Interestingly, 67% of this surface contains nonpolar solvent-accessible surface area. The success of our approach to identifying the IBS on an AFP, without considering the presence of polar side chains, indicates that flatness is the first approximation of an IBS. We further propose that the specificity of interactions between an IBS and a particular ice-crystallographic plane arises from surface complementarity.

Algorithms↗

PubMed2001

Kinetic effects of a single-amino acid mutation in a highly variable loop (residues 114-120) of class IV ADH.

Class IV alcohol dehydrogenase shows a deletion at position 117 with respect to class I enzymes, which typically have a Gly residue. In class I structures, Gly117 is part of a loop (residues 114-120) that is highly variable within the alcohol dehydrogenase family. A mutant human class IV enzyme was engineered in which a Gly residue was inserted at position 117 (G117ins). Its kinetic properties, regarding ethanol and primary aliphatic alcohols, secondary alcohols and pH profiles, were determined and compared with the results obtained in previous studies in which the size of the 114-120 loop was modified. For the enzymes considered, a smaller loop was associated with a lower catalytic efficiency towards short-chain alcohols (ethanol and propanol) and secondary alcohols, as well as with a higher K(m) for ethanol at pH 7.5 than at pH 10.0. The effect can be rationalized in terms of a more open, solvent-accessible active site in class IV alcohol dehydrogenase, which disfavors productive binding of ethanol and short-chain alcohols, specially at physiological pH.

Alcohol Dehydrogenase↗

PubMed2002

Important amino acid properties for determining the transition state structures of two-state protein mutants.

Understanding the mechanism in the folding pathways of proteins is an important problem in molecular biology. The Phi-value analysis provides insight into the transition state structures during protein folding. In this work, we have analyzed the relationship between the observed Phi values upon mutations in two-state proteins (FK506 binding protein, chymotrypsin inhibitor and src SH3 domain) and the changes in 48 various physico-chemical, energetic and conformational properties. We found that the classification of mutations based on solvent accessibility improved the correlation significantly. The relationship between conformational properties and Phi values determines the presence/absence of secondary structures in the transition state. In buried mutations, the physical properties volume, shape and flexibility, and the thermodynamic properties enthalpy, entropy and free-energy change have significant correlation with Phi. The short and medium-range non-bonded energy in partially buried mutations and average long-range contacts in exposed mutations showed a strong correlation with Phi values. Multiple regression analysis incorporating combinations of three properties from among all possible combinations of the 48 properties increased the correlation coefficient up to 0.99, by an average rise of 20% for all the data sets. Information about local sequence and structure is more important in surface mutations than those in buried mutations for explaining the transition state structures of two-state proteins. Further, the implications of our results for understanding the process of protein folding have been discussed.

Amino Acid Sequence↗

PubMed2002

Mapping of protein:protein contact surfaces by hydrogen/deuterium exchange, followed by on-line high-performance liquid chromatography-electrospray ionization Fourier-transform ion-cyclotron-resonance mass analysis.

For protein complexes too large, uncrystallizable/insoluble, or low concentration for conventional X-ray diffraction or nuclear magnetic resonance analysis, the contact surface(s) may be mapped by comparing H/2H exchange rate (and thus solvent accessibility) of backbone amide hydrogens in free vs. complexed protein(s). The protein is first exposed to 2H2O, allowed to exchange for each of several reaction periods, and then digested with pepsin. The extent and rate of H/2H exchange is determined by measuring the increase in mass with H/2H exchange period for each of the peptides. Here, we present an experimental protocol that combines rapid (to minimize back-exchange) HPLC front-end separation with ultrahigh-resolution mass analysis (needed to distinguish the isotopic distributions of dozens of peptides simultaneously). The method is used to study the assembled human immunodeficiency virus type capsid protein (CA) and its soluble form.

Amino Acid Sequence↗

PubMed2003

Aprotinin conformational distributions during reversed-phase liquid chromatography. Analysis by hydrogen-exchange mass spectrometry.

Hydrogen-exchange mass spectrometry analysis of the stable protein aprotinin during reversed-phase liquid chromatography shows both native and unfolded protein. The behavior is consistent with only two conformational states, a near-native state and a fully solvent-accessible state, with reversible interchange of species within and between the mobile and stationary phases. The amount of unfolded form is greater on C18 relative to C4 alkyl modified silica surfaces. The addition of (NH4)2SO4, Na2SO4, NaCl, or NaSCN to the mobile phase stabilized native conformation on the chromatographic surface, especially on the C4 media. Finally, the retention and the proportion of denatured form increases with added salts in anorder consistent with the lyotropic series, but reversed from that observed for small molecules.

Aprotinin↗

PubMed2003

Alpha-lactalbumin tertiary structure changes on hydrophobic interaction chromatography surfaces.

Hydrogen exchange (HX) detected by mass spectrometry (MS) was used to analyze the structure of calcium-free alpha-lactalbumin, a model protein with marginal stability. Two chromatographic peaks were observed from samples of pure protein eluted from SOURCE phenyl hydrophobic interaction chromatography (HIC) media. Whole-protein HX measurements showed that the less-retained peak had solvent exposure similar to native protein in the absence of the HIC surface while the retained protein was nearly, although not fully, solvent exposed. The formation of these two peaks was kinetically limited. The protein also refolded successfully following elution. In addition, proteolytic fragmentation was used to analyze HX at the peptide level. This approach revealed that helix C was the most stable region of alpha-lactalbumin under native conditions and in the flow-through peak. Helix C also formed the core of residual native structure in the partially unfolded protein in the retained peak. The results suggest that residues that are most solvent accessible under native conditions may be those most likely to unfold upon adsorption.

Amino Acid Sequence↗

PubMed2002

Knowledge-based design of reagentless fluorescent biosensors from recombinant antibodies.

The possibility of obtaining from any antibody a fluorescent conjugate which responds to the binding of the antigen by a variation of its fluorescence, would be of great interest in the analytical sciences and for the construction of protein chips. This possibility was explored with antibody mAbD1.3 directed against hen egg white lysozyme. Rules of design were developed to identify the residues of the antibody to which a fluorophore could be chemically coupled, after changing them to cysteine by mutagenesis. These rules were based on: the target residue belonging to a topological neighbourhood of the antigen in the structure of the complex between antibody and antigen; its absence of functional importance for the interaction with the antigen; and its solvent accessibility in the structure of the free antibody. Seventeen conjugates between the single-chain variable fragment scFv of mAbD1.3 and an environment-sensitive fluorophore were constructed. For six of the ten residues which fully satisfied the design rules, the relative variation of the fluorescence intensity between the free and bound states of the conjugate was comprised between 12 and 75% (in non-optimal buffer), and the affinity of the conjugate for lysozyme remained unchanged relative to the parental scFv. In contrast, such results were true for only one of the seven residues which failed to satisfy one of the rules and were used as controls. One of the conjugates was studied in more detail. Its fluorescence increased proportionally to the concentration of lysozyme in a nanomolar range, up to 90% in a defined buffer, and 40% in serum. This increase was specific for hen egg lysozyme and it was not observed with a closely related protein, turkey egg lysozyme. The residues which gave operational conjugates (six in V(L) and one in V(H)), were located in the immediate vicinity of residues which are functionally important, along the sequence of FvD1.3. The results suggest rules of design for constructing antigen-sensitive fluorescent conjugates from any antibody, in the absence of structural data.

Amino Acid Sequence↗