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PubMed2004

Polyproline II helix is the preferred conformation for unfolded polyalanine in water.

Does aqueous solvent discriminate among peptide conformers? To address this question, we computed the solvation free energy of a blocked, 12-residue polyalanyl-peptide in explicit water and analyzed its solvent structure. The peptide was modeled in each of 4 conformers: alpha-helix, antiparallel beta-strand, parallel beta-strand, and polyproline II helix (P(II)). Monte Carlo simulations in the canonical ensemble were performed at 300 K using the CHARMM 22 forcefield with TIP3P water. The simulations indicate that the solvation free energy of P(II) is favored over that of other conformers for reasons that defy conventional explanation. Specifically, in these 4 conformers, an almost perfect correlation is found between a residue's solvent-accessible surface area and the volume of its first solvent shell, but neither quantity is correlated with the observed differences in solvation free energy. Instead, solvation free energy tracks with the interaction energy between the peptide and its first-shell water. An additional, previously unrecognized contribution involves the conformation-dependent perturbation of first-shell solvent organization. Unlike P(II), beta-strands induce formation of entropically disfavored peptide:water bridges that order vicinal water in a manner reminiscent of the hydrophobic effect. The use of explicit water allows us to capture and characterize these dynamic water bridges that form and dissolve during our simulations.

Computer Simulation↗

PubMed1998

Structural and morphological characterization of ultralente insulin crystals by atomic force microscopy: evidence of hydrophobically driven assembly.

Although x-ray crystal structures exist for many forms of insulin, the hormone involved in glucose metabolism and used in the treatment of diabetes, x-ray structural characterization of therapeutically important long-acting crystalline ultralente insulin forms has been elusive because of small crystal size and poor diffraction characteristics. We describe tapping-mode atomic force microscopy (TMAFM) studies, performed directly in crystallization liquor, of ultralente crystals prepared from bovine, human, and porcine insulins. Lattice images obtained from direct imaging of crystal planes are consistent with R3 space group symmetry for each insulin type, but the morphology of the human and porcine crystals observed by AFM differs substantially from that of the bovine insulin crystals. Human and porcine ultralente crystals exhibited large, molecularly flat (001) faces consisting of hexagonal arrays of close packed hexamers. In contrast, bovine ultralente crystals predominantly exhibited faces with cylindrical features assignable to close-packed stacks of insulin hexamers laying in-plane, consistent with the packing motif of the (010) and (011) planes. This behavior is attributed to a twofold increase in the hydrophobic character of the upper and lower surfaces of the donut-shaped insulin hexamer in bovine insulin compared to its human and porcine counterparts that results from minor sequence differences between these insulins. The increased hydrophobicity of these surfaces can promote hexamer-hexamer stacking in precrystalline aggregates or enhance attachment of single hexamers along the c axis at the crystal surface during crystal growth. Both events lead to enhanced growth of ¿hk0¿ planes instead of (001). The insulin hexamers on the (010) and (110) faces are exposed "edge-on" to the aqueous medium, such that solvent access to the center of the hexamer and to solvent channels is reduced compared to the (001) surface, consistent with the slower dissolution and reputed unique basal activity of bovine ultralente insulin. These observations demonstrate that subtle variations in amino acid sequence can dramatically affect the interfacial structure of crystalline proteins.

Animals↗

PubMed2001

A transition-state analogue reduces protein dynamics in hypoxanthine-guanine phosphoribosyltransferase.

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is the key enzyme in purine base salvage in humans and in purine auxotrophs, including Plasmodium falciparum, the leading cause of malaria. Hydrogen/deuterium (H/D) exchange into amide bonds, quantitated by on-line HPLC and mass spectrometry, has been used to compare the dynamic and conformational properties of human HGPRT alone, the HGPRT-GMP-Mg(2+) complex, the HGPRT-IMP-MgPPi <==> HGPRT-Hx-MgPRPP equilibrating mixture, and the transition-state analogue complex HGPRT-ImmGP-MgPPi. The rate and extent of H/D exchange of 26 peptic peptides, spanning 91% of the primary structure, have been monitored. Human HGPRT has 207 amide H/D exchange sites. After 1 h in D2O, HGPRT alone exchanges 160, HGPRT-GMP-Mg(2+) exchanges 154, the equilibrium complex exchanges 139, and the transition-state analogue complex exchanges 126 of these amide protons. H/D exchange rates are correlated with structure for peptides in (1) catalytic site loops, (2) a connected peptide of the subunit interface of the tetramer, and (3) a loop buried in the catalytic site. Structural properties related to H/D exchange are defined from crystallographic studies of the HGPRT-GMP-Mg(2+) and HGPRT-ImmGP-MgPPi complexes. Transition-state analogue binding strengthens the interaction between subunits and tightens the catalytic site loops. The solvent exchange dynamics in specific peptides correlates with hydrogen bond patterns, solvent access, crystallographic B-factors, and ligand exchange rates. Solvent exchange reveals loop dynamics in the free enzyme, Michaelis complexes, and the complex with the bound transition-state analogue. Proton transfer paths, rather than dynamic motion, are required to explain exchange into a buried catalytic site peptide in the complex with the bound transition-state analogue.

Amino Acid Sequence↗

PubMed2003

Discrimination of native protein structures using atom-atom contact scoring.

We introduce a method for discriminating correctly folded proteins from well designed decoy structures using atom-atom and atom-solvent contact surfaces. The measure used to quantify contact surfaces integrates the solvent accessible surface and interatomic contacts into one quantity, allowing solvent to be treated as an atom contact. A scoring function was derived from statistical contact preferences within known protein structures and validated by using established protein decoy sets, including the "Rosetta" decoys and data from the CASP4 structure predictions. The scoring function effectively distinguished native structures from all corresponding decoys in >90% of the cases, using isolated protein subunits as target structures. If contacts between subunits within quaternary structures are included, the accuracy increases to 97%. Interactions beyond atom-atom contact range were not required to distinguish native structures from the decoys using this method. The contact scoring performed as well or better than existing statistical and physicochemical potentials and may be applied as an independent means of evaluating putative structural models.

Cations↗

PubMed1996

Sequence-specific DNA-binding dominated by dehydration.

Fluorescence spectroscopy and isothermal titration calorimetry were used to study the thermodynamics of binding of the glucocorticoid receptor DNA-binding domain to four different, but similar, DNA-binding sites. The binding sites are two naturally occurring sites that differ in the composition of one base pair, i.e., an A-T to G-C mutation, and two sites containing chemical intermediates of these base pairs. The calorimetrically determined heat capacity change (Delta C(p)o(obs)) for glucocorticoid receptor DNA-binding domain binding agrees with that calculated for dehydration of solvent-accessible surface areas. A dominating effect of dehydration or solvent reorganization on the thermodynamics is also consistent with an observed linear relationship between observed enthalpy change (Delta Ho(obs)) and observed entropy change (Delta So(obs)) with a slope close to the experimental temperature. Comparisons with structural data allow us to rationalize individual differences between Delta Ho(obs) (and Delta So(obs)) for the four complexes. For instance, we find that the removal of a methyl group at the DNA-protein interface is enthalpically favorable but entropically unfavorable, which is consistent with a replacement by an ordered water molecule.

Animals↗

PubMed2005

Conformational dynamics of amyloid beta-protein assembly probed using intrinsic fluorescence.

Formation of toxic oligomeric and fibrillar structures by the amyloid beta-protein (Abeta) is linked to Alzheimer's disease (AD). To facilitate the targeting and design of assembly inhibitors, intrinsic fluorescence was used to probe assembly-dependent changes in Abeta conformation. To do so, Tyr was substituted in Abeta40 or Abeta42 at position 1, 10 (wild type), 20, 30, 40, or 42. Fluorescence then was monitored periodically during peptide monomer folding and assembly. Electron microscopy revealed that all peptides assembled readily into amyloid fibrils. Conformational differences between Abeta40 and Abeta42 were observed in the central hydrophobic cluster (CHC) region, Leu17-Ala21. Tyr20 was partially quenched in unassembled Abeta40 but displayed a significant and rapid increase in intensity coincident with the maturation of an oligomeric, alpha-helix-containing intermediate into amyloid fibrils. This process was not observed during Abeta42 assembly, during which small decreases in fluorescence intensity were observed in the CHC. These data suggest that the structure of the CHC in Abeta42 is relatively constant within unassembled peptide and during the self-association process. Solvent accessibility of the Tyr ring was studied using a mixed solvent (dimethyl sulfoxide/water) system. [Tyr40]Abeta40, [Tyr30]Abeta42, and [Tyr42]Abeta42 all were relatively shielded from solvent. Analysis of the assembly dependence of the site-specific intrinsic fluorescence data suggests that the CHC is particularly important in controlling Abeta40 assembly, whereas the C-terminus plays the more significant role in Abeta42 assembly.

Alzheimer Disease↗

PubMed2005

Scanning cysteine mutagenesis analysis of Abeta-(1-40) amyloid fibrils.

We describe here the use of cysteine substitution mutants in the Alzheimer disease amyloid plaque peptide Abeta-(1-40) to probe amyloid fibril structure and stabilization. In one approach, amyloid fibrils were grown from Cys mutant peptides under reducing conditions and then challenged with an alkylating agent to probe solvent accessibility of different residues in the fibril. In another approach, monomeric Cys mutants, either in the thiol form or modified with iodoacetic acid or methyl iodide, were grown into amyloid fibrils, and the equilibrium position at the end of the amyloid formation reaction was quantified by determining the concentration of monomeric Abeta. The DeltaG values of fibril elongation obtained were then compared in order to provide information on the environment of each residue side chain in the fibril. In general, Cys residues in the N and C termini of Abeta-(1-40) were not only accessible to alkylation in the fibril state but also, when modified in the monomeric state, did not greatly impact fibril stability; these observations were consistent with previous indications that these portions of the peptide are not part of the amyloid core. In contrast, residues 16-19 and 31-34 were not only uniformly inaccessible to alkylation in the fibril state, but their modification with the negatively charged carboxymethyl group in monomeric Abeta also destabilized fibril elongation, confirming other data showing that these segments are likely packed into a hydrophobic amyloid core. Residues 20, 30, and 35, flanking these implicated beta-sandwich regions, are accessible to alkylation in the fibril indicating a location in solvent exposed structure.

Amino Acid Sequence↗

PubMed2004

NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity.

The deletion mutant Delta(7-22) of alpha-sarcin, unlike its wild-type protein counterpart, lacks the specific ability to degrade rRNA in intact ribosomes and exhibits an increased unspecific ribonuclease activity and decreased interaction with lipid vesicles. In trying to shed light on these differences, we report here on the three-dimensional structure of the Delta(7-22) alpha-sarcin mutant using NMR methods. We also evaluated its dynamic properties on the basis of theoretical models and measured its correlation time (6.2 nsec) by time-resolved fluorescence anisotropy. The global fold characteristic of ribotoxins is preserved in the mutant. The most significant differences with respect to the alpha-sarcin structure are concentrated in (1) loop 2, (2) loop 3, which adopts a new orientation, and (3) loop 5, which shows multiple conformations and an altered dynamics. The interactions between loop 5 and the N-terminal hairpin are lost in the mutant, producing increased solvent accessibility of the active-site residues. The degree of solvent exposure of the catalytic His 137 is similar to that shown by His 92 in RNase T1. Additionally, the calculated order parameters of residues belonging to loop 5 in the mutant correspond to an internal dynamic behavior more similar to RNase T1 than alpha-sarcin. On the other hand, changes in the relative orientation of loop 3 move the lysine-rich region 111-114, crucial for substrate recognition, away from the active site. All of the structural and dynamic data presented here reveal that the mutant is a hybrid of ribotoxins and noncytotoxic ribonucleases, consistent with its biological properties.

Aspergillus↗

PubMed1992

The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures.

To characterize water binding to proteins, which is fundamental to protein folding, stability and activity, the relationships of 10,837 bound water positions to protein surface shape and residue type were analyzed in 56 high-resolution crystallographic structures. Fractal atomic density and accessibility algorithms provided an objective characterization of deep grooves in solvent-accessible protein surfaces. These deep grooves consistently had approximately the diameter of one water molecule, suggesting that deep grooves are formed by the interactions between protein atoms and bound water molecules. Protein surface topography dominates the chemistry and extent of water binding. Protein surface area within grooves bound three times as many water molecules as non-groove surface; grooves accounted for one-quarter of the total surface area yet bound half the water molecules. Moreover, only within grooves did bound water molecules discriminate between different side-chains. In grooves, main-chain surface was as hydrated as that of the most hydrophilic side-chains, Asp and Glu, whereas outside grooves all main and side-chains bound water to a similar, and much decreased, extent. This identification of the interdependence of protein surface shape and hydration has general implications for modelling and prediction of protein surface shape, recognition, local folding and solvent binding.

Algorithms↗

PubMed1993

HLA-B*0702 antibody epitopes are affected indirectly by distant antigen residues.

We examine the effect of mutations in the HLA-B*0702 alpha 1 domain on the binding of several well-characterized monoclonal antibodies. BB7.1 recognizes the alpha-helix, with a special requirement for residue 67. Combined with an established requirement for the alpha 2 alpha-helix, BB7.1 appears to span the B*0702 peptide-binding groove. Alternatively, BB7.1 epitope conformation may be altered by distant B*0702 sites. ME1 and B27M1 recognize connecting loop residues 41 and 43 and alpha 1 alpha-helical residues 67-71. Instead of contacting residue 67-71 side chains directly, however, ME1 appears to recognizes a B*0702 configuration that depends upon the proper interaction of these and other HLA residues. In addition to solvent-accessible residues 41 and 43, the B27M1 epitope depends on solvent-inaccessible residue 32 at the bottom of the peptide-binding groove. MB40.2, known to require residues 169-182 near the alpha 2-alpha 3 junction, also requires the proper combination of distant residues in the alpha 1 beta-strand and alpha-helix. The effect of mutations near the peptide-binding groove suggests that bound peptides may directly or indirectly affect HLA epitopes. These results illustrate that HLA epitope conformation is very sensitive to changes at distant HLA sites and forecast that epitope models based on sequential amino acid residues will often fail to predict HLA epitopes.

Animals↗

PubMed2006

Crucial importance of translational entropy of water in pressure denaturation of proteins.

We present statistical thermodynamics of pressure denaturation of proteins, in which the three-dimensional integral equation theory is employed. It is applied to a simple model system focusing on the translational entropy of the solvent. The partial molar volume governing the pressure dependence of the structural stability of a protein is expressed for each structure in terms of the excluded volume for the solvent molecules, the solvent-accessible surface area (ASA), and a parameter related to the solvent-density profile formed near the protein surface. It is argued that the entropic effect originating from the translational movement of water molecules plays critical roles in the pressure-induced denaturation. We also show that the exceptionally small size of water molecules among dense liquids in nature is crucial for pressure denaturation. An unfolded structure, which is only moderately less compact than the native structure but has much larger ASA, is shown to turn more stable than the native one at an elevated pressure. The water entropy for the native structure is higher than that for the unfolded structure in the low-pressure region, whereas the opposite is true in the high-pressure region. Such a structure is characterized by the cleft and/or swelling and the water penetration into the interior. In another solvent whose molecular size is 1.5 times larger than that of water, however, the inversion of the stability does not occur any longer. The random coil becomes relatively more destabilized with rising pressure, irrespective of the molecular size of the solvent. These theoretical predictions are in qualitatively good agreement with the experimental observations.

Entropy↗

PubMed2005

Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus.

The crystal structure of the vitamin B(6)-dependent enzyme phosphoserine aminotransferase from the obligatory alkaliphile Bacillus alcalophilus has been determined at 1.08 A resolution. The model was refined to an R-factor of 11.7% (R(free) = 13.9%). The enzyme displays a narrow pH optimum of enzymatic activity at pH 9.0. The final structure was compared to the previously reported structure of the mesophilic phosphoserine aminotransferase from Escherichia coli and to that of phosphoserine aminotransferase from a facultative alkaliphile, Bacillus circulans subsp. alkalophilus. All three enzymes are homodimers with each monomer comprising a two-domain architecture. Despite the high structural similarity, the alkaliphilic representatives possess a set of distinctive structural features. Two residues directly interacting with pyridoxal-5'-phosphate are replaced, and an additional hydrogen bond to the O3' atom of the cofactor is present in alkaliphilic phosphoserine aminotransferases. The number of hydrogen bonds and hydrophobic interactions at the dimer interface is increased. Hydrophobic interactions between the two domains in the monomers are enhanced. Moreover, the number of negatively charged amino acid residues increases on the solvent-accessible molecular surface and fewer hydrophobic residues are exposed to the solvent. Further, the total amount of ion pairs and ion networks is significantly reduced in the Bacillus enzymes, while the total number of hydrogen bonds is increased. The mesophilic enzyme from Escherichia coli contains two additional beta-strands in a surface loop with a third beta-strand being shorter in the structure. The identified structural features are proposed to be possible factors implicated in the alkaline adaptation of phosphoserine aminotransferase.

Adaptation, Physiological↗

PubMed2000

Site-directed sulfhydryl labeling of the lactose permease of Escherichia coli: helix X.

Helix X in the lactose permease of Escherichia coli contains two residues that are irreplaceable with respect to active transport, His322 and Glu325, as well as Lys319, which is charge-paired with Asp240 in helix VII. Structural and dynamic features of transmembrane helix X are investigated here by site-directed thiol modification of 14 single-Cys replacement mutants with N-[(14)C]ethylmaleimide (NEM) in right-side-out membrane vesicles. Permease mutants with a Cys residue at position 326, 327, 329, 330, or 331 in the cytoplasmic half of the transmembrane domain are alkylated by NEM at 25 degrees C, a mutant with Cys at position 315 at the periplasmic surface is labeled in the presence of substrate exclusively, and mutants with Cys at positions 317, 318, 320, 321, 324, 328, 332, or 333 do not react with NEM under the conditions tested. Binding of substrate causes increased labeling of a Cys residue at position 315 and decreased labeling of Cys residues at positions 326, 327, and 329. Studies with methanethiosulfonate ethylsulfonate indicate that Cys residues at positions 326, 329, 330, and 331 in the cytoplasmic half are accessible to the aqueous phase from the periplasmic face of the membrane. Ligand binding results in clear attenuation of solvent accessibility of Cys at position 326 and a marginal increase in accessibility of Cys at position 327 to solvent. The findings indicate that the cytoplasmic half of helix X is more reactive/accessible to thiol reagents and more exposed to solvent than the periplasmic half. Furthermore, positions that reflect ligand-induced conformational changes are located on the same face of helix X as Lys319, His322, and Glu325.

Amino Acid Sequence↗

PubMed2001

Prediction of protein surface accessibility with information theory.

A new, simple method based on information theory is introduced to predict the solvent accessibility of amino acid residues in various states defined by their different thresholds. Prediction is achieved by the application of information obtained from a single amino acid position or pair-information for a window of seventeen amino acids around the desired residue. Results obtained by pairwise information values are better than results from single amino acids. This reinforces the effect of the local environment on the accessibility of amino acid residues. The prediction accuracy of this method in a jackknife test system for two and three states is better than 70 and 60 %, respectively. A comparison of the results with those reported by others involving the same data set also testifies to a better prediction accuracy in our case.

Algorithms↗

PubMed2002

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

The development and parameterization of a solvent potential of mean force designed to reproduce the hydration thermodynamics of small molecules and macromolecules aimed toward applications in conformation prediction and ligand binding free energy prediction is presented. The model, named SGB/NP, is based on a parameterization of the Surface Generalized Born continuum dielectric electrostatic model using explicit solvent free energy perturbation calculations and a newly developed nonpolar hydration free energy estimator motivated by the results of explicit solvent simulations of the thermodynamics of hydration of hydrocarbons. The nonpolar model contains, in addition to the more commonly used solvent accessible surface area term, a component corresponding to the attractive solute-solvent interactions. This term is found to be important to improve the accuracy of the model, particularly for cyclic and hydrogen bonding compounds. The model is parameterized against the experimental hydration free energies of a set of small organic molecules. The model reproduces the experimental hydration free energies of small organic molecules with an accuracy comparable or superior to similar models employing more computationally demanding estimators and/or a more extensive set of parameters.

Algorithms↗

PubMed1980

Individual breathing reactions measured in hemoglobin by hydrogen exchange methods.

Protein hydrogen exchange is generally believed to register some aspects of internal protein dynamics, but the kind of motion at work is not clear. Experiments are being done to identify the determinants of protein hydrogen exchange and to distinguish between local unfolding and accessibility-penetration mechanisms. Results with small molecules, polynucleotides, and proteins demonstrate that solvent accessibility is by no means sufficient for fast exchange. H-exchange slowing is quite generally connected with intramolecular H-bonding, and the exchange process depends pivotally on transient H-bond cleavage. At least in alpha-helical structures, the cooperative aspect of H-bond cleavage must be expressed in local unfolding reactions. Results obtained by use of a difference hydrogen exchange method appear to provide a direct measurement of transient, cooperative, local unfolding reactions in hemoglobin. The reality of these supposed coherent breathing units is being tested by using the difference H-exchange approach to tritium label the units one at a time and then attempting to locate the tritium by fragmenting the protein, separating the fragments, and testing them for label. Early results demonstrate the feasibility of this approach.

Deuterium↗

PubMed1987

Properties of covalent benzo[a]pyrene diol epoxide-DNA adducts investigated by fluorescence techniques.

The spectroscopic absorption and fluorescence properties of adducts derived from the covalent binding of (+/-)trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyre ne (BPDE) to DNA are re-examined in view of conflicting interpretations regarding the conformations of these adducts which currently exist in the literature. The fluorescence decay profiles were accurately determined utilizing synchrotron-pulsed light source excitation and the time-correlated single photon counting technique. The conformational properties of the adducts were probed by determining their accessibilities to acrylamide, a known fluorescence quencher, and by comparing the accessibilities of the BPDE-DNA adducts with those of known model systems with intercalative, partially intercalative and minor groove binding conformations. In contrast to any of these model systems, the fluorescence of the aromatic pyrenyl residues in the covalent BPDE-DNA adducts exhibit significant sensitivity to acrylamide, suggesting that these residues are located at binding sites with significant solvent exposure. A quantitative analysis of the acrylamide fluorescence quenching according to a dynamic Stern-Volmer quenching model suggests the following characteristics: the major (65%) component (1.4 ns lifetime) is characterized by significant exposure to the solvent environment; the second component (6-7 ns lifetime) can be subdivided into a solvent-accessible and a solvent-inaccessible component, the inaccessible fraction being attributed to minor adducts, possibly with a quasi-intercalative conformation. The amplitude of the third, long-lived (200-ns) component is variable; it arises from the photochemical decomposition of the adducts which gives rise to tetraols (7,8,9,10-tetrahydro-tetrahydroxybenzo[a]pyrene). The variable content of these degradation products accounts for most discrepancies in the fluorescence properties of the covalent BPDE-DNA adducts previously reported.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

PubMed1989

Conformations of dehydrophenylalanine containing peptides: nmr studies of an acyclic hexapeptide with two delta Z-Phe residues.

The conformation of an acyclic dehydrophenylalanine (delta Z-Phe) containing hexapeptide, Boc-Phe-delta Z-Phe-Val-Phe-delta Z-Phe-Val-OMe, has been investigated in CDCl3 and (CD3)2SO by 270-MHz 1H-nmr. Studies of NH group solvent accessibility and observation of interresidue nuclear Overhauser effects (NOEs) suggest a significant solvent-dependent conformational variability. In CDCl3, a population of folded helical conformations is supported by the inaccessibility to solvent of the NH groups of residues 3-6 and the detection of several NiH----Ni + 1H NOEs. Evidence is also obtained for conformational heterogeneity from the detection of some Ci alpha H----Ni + 1H NOEs characteristic of extended strands. In (CD3)2SO, the peptide largely favors an extended conformation, characterized by five solvent-exposed NH groups and successive Ci alpha H----Ni + 1H NOEs for the L-residues and Ci beta H----Ni + 1H NOEs for the delta Z-Phe residues. The results suggest that delta Z-Phe residues do not provide compelling conformational constraints.

Magnetic Resonance Spectroscopy↗