bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
Authors: Gilson Michael K. , Honig Barry 
Published: May 2005

AbstractIn this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in proteins as well as changes in solvation energy that accompany the binding of charged substrates. The validity of the method is examined by calculating the hydration energies of acetate, methyl ammonium, ammonium, and methanol. The method is then used to study the relationship between the depth of a charge within a protein and its interaction with the solvent. Calculations of the relative electrostatic energies of crystal and misfolded conformations of Themiste dyscritum hemerythrin and the VL domain of an antibody are also presented. The results indicate that electrostatic charge‐solvent interactions strongly favor the crystal structures. More generally, it is found that charge‐solvent interactions, which are frequently neglected in protein structure analysis, can make large contributions to the total energy of a macromolecular system.
Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system
Authors: Dauber‐Osguthorpe Pnina , Roberts Victoria A. , Osguthorpe David J. , Wolff Jon , Genest Moniqe , Hagler Arnold T. 
Published: May 2005

AbstractA study of the binding of the antibacterial agent trimethoprim to Escherichia coli dihydrofolate reductase was carried out using energy minimization techniques with both a full, all‐atom valence force field and a united atom force field. Convergence criteria ensured that no significant structural or energetic changes would occur with further minimization. Root‐mean‐square (RMS) deviations of both minimized structures with the experimental structure with the experimental structure were calculated for selected regions of the protein. In the active site, the all‐atom minimized structure fit the experimental structure much better than did the united atom structure. To ascertain what constitutes a good fit, the RMS deviations between crystal structures of the same enzyme either from different species or in different crystal environments were compared. The differences between the active site of all‐atom minimized structure and the experimental structure are similar to differences observed between crystal structures of the same protein.Finally, the energetics of ligand binding were analyzed for the all‐atom minimized coordinates. Strain energy induced in the ligand, the corresponding entropy loss due to shifts in harmonic frequencies, and the role of specific residues in ligand binding were examined. Water molecules, even those not in direct contact with the ligand, were found to have significant interaction energies with the ligand. Thus, the inclusion of at least one shell of waters may be vital for accurate simulations of enzyme complexes.
Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences
Authors: McCaldon Peter , Argos Patrick 
Published: May 2005

AbstractWe have examined oligopeptides with lengths ranging from 2 to 11 residues in protein sequences that show no obvious evolutionary relationship. All sequences in the Protein Identification Resource database were carefully classified by sensitive homology searches into superfamilies to obtain unbiased oligopeptide counts. The results, contrary to previous studies, show clear prejudices in protein sequences. The oligopeptide preferences were used to help decide the significance of sequence homologies and to improve the more general methods for detecting protein coding regions within nucleotide sequences.
Surface interactions of γ‐crystallins in the crystal medium in relation to their association in the eye lens
Authors: Sergeev Y. V. , Chirgadze Y. N. , Mylvaganam S. E. , Driessen H. , Slingsby C. , Blundell T. L. 
Published: May 2005

AbstractA comparative study of intermolecular interactions in crystals of two homologous low molecular weight proteins, γ‐II and γ‐IIIb crystallins, from calf eye lens was carried out. Crystal packings for these proteins are very different: intermolecular contact areas compose about 33% of the total accessible surface area of γ‐II as compared with 13% in γ‐III. Two key residues seem to be mainly responsible for the differences in protein association in the crystal medium. These are Ser 103 and Leu 155 in γ‐II, which are replaced by Met 103 and His 155 in γ‐IIIb. A similar substitution of these residues is observed in different gene products of γ‐crystallins from a number of vertebrates. This is consistent with the existence of a genetically controlled mechanism for determining intermolecular association of γ‐crystallins in the native medium of the lens.
Interaction of peptide boronic acids with elastase: Circular dichroism studies
Authors: Berry S. C. , Fink Anthony L. , Shenvi A. B. , Kettner C. A. 
Published: May 2005

AbstractBoronic acid derivatives of good peptide substrate of the serine proteases cause slow‐binding inhibition, manifested as biphasic binding (Kettner and Shenvi: J. Biol. Chem. 259:15106–15114, 1984). These inhibitors are thought to act as reaction‐intermediate analogs. Three peptides Boronic acids—Ac‐Pro‐boro‐Val‐OH, DNS‐Ala‐Pro‐boro‐Val‐OH, and Ac‐Ala‐Ala‐Pro‐boro‐Val‐OH—were chosen for farultraviolet circular dichroism (CD) studies in order to determine whether the second phase involves a conformational change of pancreatic elastase. The dipeptide is a simple competitive inhibitors (Ki = 0.27 μM) and the latter are slow‐binding inhibitors (Ki = 16.4 and 0.25 nM, respectively). Spectral deconvolution and correction for the formation of antiparallel β‐sheet by the peptide inhibitors itself indicate that there is no significant change in the secondary structure of the enzyme in the either the initial or final inhibitors complex. A kinetic experiment confirmed that the slow‐binding step was not associated with a CD spectral change, and that therefore a protein conformational change was not responsible for the sow binding.
Diffusion‐collision model for the folding kinetics of myoglobin
Authors: Bashford Donald , Cohen F. E. , Karplus M. , Kuntz I. D. , Weaver D. L. 
Published: May 2005

AbstractThe diffusion‐collision model has been used to analyze the folding kinetics of myoglobins. The microdomains, which are the basic units that coalesce during the folding, are identified with the helices and the stabilizing contacts between helices are determined form the native structure. Both association and disassociation reactions are included and a range of stabilization parameters is investigated to determine the variations in overall rate and the relative contributions made by the different intermediates during the folding process. In a comparison of folding to the native state and to the midpoint of the folding transitions. (i.e., 50% native protein at the completion of the reaction) significant differences in the contributing intermediates are found.
Further experimental studies of the disulfide folding transition of ribonuclease A
Authors: Wearne Steven J. , Creighton Thomas E. 
Published: May 2005

AbstractTwo very different mechanisms of folding have been proposed from experimental studies of disulfide formation in reduced ribonuclease A. (1) A pathway in which the rate‐limiting step separates fully folded protein from all other disulfide intermediates and occurs solely in three‐disulfide intermediates. (2) A multiple pathway mechanism with different rate‐limiting steps for each pathway. The various rate‐limiting steps involve disulfide breakage, formation, and rearrangement in intermediates with one, two, three, and four protein disulfides. To distinguish between these two mechanisms, we have carried out further studies of both unfolding and refolding.Refolding of reduced ribonuclease A requires three‐disulfide intermediates to accumulate; negligible refolding occurs when only the nearly random one‐ and two‐disulfide intermediate species are populated. Therefore, no rate‐limiting steps of the type postulated in mechanism (2) occur in intermediates with one and two protein disulfides. Unfolding and disulfide reduction is an all‐or‐none process; no disulfide intermediates accumulate to detectable to detectable levels or precede the rate‐limiting step. Mechanism (2) requires that such intermediates precede the rate‐limiting step and accumulate to substantial levels.The different proposal were shown not to result from the use of different solution conditions or disulfide reagents; the two sets of data are not inconsistent. Instead, the inappropriate mechanism (2) resulted from an incorrect kinetic analysis and misinterpretation of the kinetics of disulfide formation are breakage.
Further studies of the helix dipole model: Effects of a free α‐NH3+ or α‐COO− group on helix stability
Authors: Fairman Robert , Shoemaker Kevin R. , York Eunice J. , Stewart Jhon M. , Baldwin Robert L. 
Published: May 2005

AbstractInteractions between the α‐helix peptide dipoles and charged groups close to the ends of the helix were found to be an important determinant of α‐helix stability in a previous study.1 The charge on the N‐terminal residue of the C‐peptide from ribonuclease A was varied chiefly by changing the α‐NH2 blocking group, and the correlation of helix stability with N‐terminal charge was demonstrated. An alternative explanation for some of those results is that the succinyl and acetyl blocking groups stabilize the helix by hydrogen bonding to an unsatisfied main‐chain NH group. The helix dipole model is tested here with peptides that contain either a free α‐NH α‐COO− groups, and no other charged groups that would titrate with similar pKa's. This model predicts that α‐NH3α‐COO‐ groups are helix‐destabilizingand that the destabilizing interactions are electrostatic in origin. The hydrogen bonding model predicts that α‐NH3 and α‐COO‐ groups are not themselves helix‐destabilizing, but that an acetyl or amide blocking group at the N‐ or C‐ terminus, respectively, stabilizes the helix by hydrogen bonding to an unsatisfied main‐chain NH or CO group.The results are as follows: (1) Removal of the charge from α‐NH3 and α‐COO‐ groups by pH titration stabilizes an α‐helix. (2) The increase in helix stability on pH titration of these groups is close to the increase produced by adding an acetyl or amide blocking group. (3) The helix‐stabilizing effect of removing the charge from α‐NH3 and α‐COO‐ groups by pH titration is screened by increasing the NaCl concentration, and therefore the effect is electrostatic in origin. (4) Replacing the C‐terminal amide blocking group with a methylester blocking group, which cannot donate a hydrogen bond, causes little change in helix stability.
Effect of protein conformation on rate of deamidation: Ribonuclease A
Authors: Wearne Steven J. , Creighton Thomas E. 
Published: May 2005

AbstractThe effect of the folded conformation of a protein on the rate of deamidation of a specific asparaginyl residue has been determine. Native and unfolded ribonuclease A (RNase A) could be compared under identical conditions, because stable unfolded protein was generated by breaking irreversibly the protein disulfide bonds.Deamidation of the labile Asn‐67 residue of RNase A was followedelectrophoretically and chromatographically. At 80°C, similar rates of deamidation were observed for the disulfidebonded form, which is thermally unfolded, and the reduced form. At 37°C and pH 8, however, the rate of deamidation of native RNase A was negligible, and was more than 30‐fold slower than that of reduced, unfolded RNase A. This demonstrates that the Asn‐67 residue is located in a local conformation in the native protein that greatly inhibits deamidation. This conformation is the β‐turn of residues 66–68.
Structure and thermal stability of monomeric bacteriorhodopsin in mixed pospholipid/detergent micelles
Authors: Brouillette Christie G. , McMichens Ruth B. , Stern Lawrence J. , Khorana H. Gobind 
Published: May 2005

AbstractThermal unfolding experiments on bacteriorhodopsin in mixed Phospholipid/detergent micelles were performed. Bacteriorhodopsin was extracted from the purple membrane in a denatured state and then renatured in the micellar system. The purpose of this study was to compare the changes, if any, in the structure and stability of a membrane protein that has folded in a nonnative environment with results obtained on the native system, i.e., the purple membrane. The purple membrane crystalline lattice is an added factor that may influence the structural stability of bacteriorhodopsin. Micelles containing bacteriorhodopsin are uniformly sized disks 105 ± 13 Å in diameter (by electron microscopy) and have an estimated molecular mass of 210 kDa (by gel filtration HPLC). The near‐UV CD spectra (which is indicative of tertiary structure) for micellar bacteriorhodopsin and the purple membrane are very similar. In the visible CD region of retinal absorption, the double band seen in the spectrum of the purple membrane is replaced with a broad positive band for micellar bacteriorhodopsin, indicating that in micelles, bacteriorhodopsin is monomeric. The plot of denaturational temperature vs. pH for micellar bacteriorhodopsin is displaced downward on the temperature axis, illustrating the lower thermal stability of micellar bacteriorhodopsin when compared to the purple membrane at the same pH. Even though micellar bacteriorhodopsin is less stable, similar changes in response to pH and temperature are seen in the visible absorption spectra of micellar bacteriorhodopsin and the purple membrane. This demonstrates that changes in the protonation state or temperature have a similar affect on the local environment of the chromophore and the protein conformation. We conclude that the tertiary structure of the bacteriorhodopsin monomer is essentially the same in micelles and the purple membrane. On the other hand, in the synthetic mixed micelle system, the packing between the nonnative amphiphiles and bacteriorhodopsin is probably not optimal, protein‐protein interactions have been lost, and thehelical packing may be looser because the crystalline lattice is absent. Itis likely that a combination of these effects leads to the decreased stability of micellar bacteriorhodopsin.
Prediction of the conformation of ice‐nucleation protein by conformational energy calculation
Authors: Mizuno Hiroshige 
Published: May 2005

AbstractThe active conformation of an icenucleation protein, whose major portion consists of a long polypeptide segment of nearly repetitive octapeptides, is predicted by the analyses of conformational energy and the mechanism of crystal growth. The protein ideally has an exact octapeptide repetition and is assumed to have a helical conformation. The present study searched for low‐energy helical conformations and each of the obtained low‐energy conformations examined as to whether it has a surface structure that can promote crystal formation. Two conformations obtained were good candidates for an ice nucleus. Both were found to have on their surfaces an arrangement of hydrogen‐bonding sites, which fits well with those of hydrogen bonds in hexagonal ice crystal. Further, one of the two conformations had a hexagonal conformational symmetry consistent with the hexagonal ice crystal structure. The other conformation had apentagonal conformational symmetry that could enable the growth of an ice crystal–dendritic polycrystalline snow crystal–which grows on metastable cubic ice.
Folding of bovine growth hormone is consistent with the molten globule hypothesis
Authors: Brems David N. , Havel Henry A. 
Published: May 2005

AbstractPrevious results from equilibrium and kinetic studies of the folding of bovine growth hormone (bGH) have demonstrated that bGH does not follow a simple two‐step folding mechanism. These results are summarized and interpreted according to the “molten globule” model. The molten globule state of bGH is characterized as a folding intermediate which largely a‐helical, retains a compact hydrodynamic radius, has packing of the aromatic side chains that is similar to the unfolded state, and possesses a solvent‐exposed hydrophobic surface along helix 106127 that readily leads association.
Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations
Authors: Noguti Tosiyuki , Gō Nobuhiro 
Published: May 2005

AbstractAn analysis is carried out of differences in the minimum energy conformations obtained in the previous paper by energy minimization starting from conformations sampled by a Monte Carlo simulation of conformational fluctuations in the native state of a globular protein, bovine pancreatictrypsin inhibitor. Main conformational differences in each pair of energy minima are found usually localized in several side chains and in a few localmain chain segments. Such side chains and local main chain segments are found to take a few distinct local conformations in the minimum energy conformations. Energy minimum conformations can thus be described in terms of combinations of these multiple local conformations.
Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations
Authors: Noguti Tosiyuki , Gō Nobuhiro 
Published: May 2005

AbstractDifferences in atom packing are studied in the minimum energy conformations derived from the record of the Monte Carlo simulation of conformational fluctuation in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations observed among the minima which are found in the previous paper are accompanied by rearrangement of atom packing. Spatial locations of the local deformations in the three‐dimensional folded structure are also studied. It is foundthat the local deformations are distributed in space in several clusters inthe folded structure. The size and location of the clusters characterize the respective fluctuations of the first and the second levels observed in the simulation. In the fluctuations of the first level local deformations, each of which usually involves a few side chains and one main chain local segment, are thermally exited independently of each other near thesurface of the molecule. The observed fluctuation of the second level involves a cooperative deformation involving many side chains and local main chain segments all in one cluster, which goes though the core of the molecule. The collective local deformations observed both in the first and second levels are plastic in the sense that they are accompanied with rearrangement of atom packing.
Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations
Authors: Noguti Tosiyuki , Gō Nobuhiro 
Published: May 2005

AbstractDistances between centers of gravity of individual residues are compared among the minimum energy conformations derived from the recordof the Monte Carlo simulation of conformational fluctuations in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations originating from the multiplicity of localconformations cause deformations of the whole structure of the molecule in various ways, which can be classified into two types. Type 1:When a local deformation occurs in a region consisting of a few residues near the surfaceof the molecule, the whole shape of the molecule responds by deforming elastically. The magnitude of this deformation is in the range of thermalfluctuations calculated by the harmonic approximation around a singleminimum. Type 2: We have observed one case belonging to the second type in which local deformations occur cooperatively in an extended region. This regiongoes across the whole molecule and divide the remaining parts into two. Atom packing changes in and around the extended region of local deformations. For this reason deformation in this region is plastic. Relative locationand orientation between the divided two parts change very much. Deformationof the whole shape in this case, associated with the plastic deformationin an extended region, demonstrates that protein molecules have a flexibility beyond the harmonic limit.
Rebuilding flavodoxin from Cα coordinates: A test study
Authors: Reid Lorne S. , Thornton Janet M. 
Published: May 2005

AbstractThe tertiary structure of flavodoxin has been model build from only the X‐ray crystallographic α‐carbon coordinates. Main‐Chain atoms were generated from a dictionary of backbone structures. Side‐chain conformations were initially set according to observed statistical distributions, clashes were resolved with reference to other knowledge‐based parameters, and finally, energy minimization was applied. The RMSD of the model was 1.7 Å across all atoms to the native structure. Regular secondary structural elements were modeledmore accurately than other regions. About 40%of the ξ1 torsional angles were modeled correctly. Packing of side chains in the core was energetically stable but diverged significantly from the native structure in some regions.The modeling of protein structures is increasing in popularity but relatively few checks have been applied to determine the accuracy of the approach. In this work a variety of parameters have been examined. It was found that close contact, and hydrogen‐bonding patterns could identifypoorly packed residues. These tests, however, did not indicate which residues had a conformation different from the native structure or how to move such residues to bring them into agreement. To assist in the modeling of interacting side chains a database of known interactions has been prepared.
Amino acid substitutions that increase the thermal stability of the λ Cro protein
Authors: Pakula Andrew A. , Sauer Robert T. 
Published: May 2005

AbstractA mutant Cro protein, which bears the Ile‐30→ Leu substitution, is thermally unstable and degraded more rapidly than wildtype Cro in vivo. Using an antibody screen, we have isolated five different second site suppressor substitutions that reduce the proteolytic hypersensitivity of this mutant Cro protein. Two of the suppressor substitutions increase the thermal stability of Cro by 12°C to 14°C. These amino acid substitutions affect residues 16 and 26, which are substitutions affect residues 16 and 26, which are substantially exposed to solvent in the crystal structure of wild‐type Cro.