bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic analysis of the molecular basis for β‐adrenergic receptor subtype specificity
Authors: Dixon Richard A. F. , Hill Wendy S. , Candelore Mari R. , Rands Elaine , Diehl Ronald E. , Marshall Mark S. , Sigal Irving S. , Strader Catherine D. 
Published: May 2005

AbstractPharmacological analysis of ligand binding to the β‐adrenergic receptor (βAR) has revealed the existence of two distinct receptor subtypes (β1 and β2) which are the products of different genes. The predicted amino acid sequence of the β1 and β2 receptors differ by 48%. To identify the regions of the proteins responsible for determining receptor subtype, chimeras were constructed from domains of the human β1 and hamster β2 receptors. Analyses of the ligand‐binding characteristics of these hybrid receptors revealed that residues in the middle portion of the βAR sequence, particularly around transmembrane regions 4 and 5, contribute to the subtype specific binding of agonists. Smaller molecular replacement of regions of the hamster β2AR with the analogous regions from the avian β1AR, however, failed to identify any single residue substitution capable of altering the subtype specificity of the receptor. These data indicate that, whereas sequences around transmembrane regions 4 and 5 may contribute to conformations which influence the ligand‐binding properties of the receptor, the subtype‐specific differences in amine‐substituted agonist binding cannot be attributed to a single molecular interaction between the ligand and any amino acid residue which is divergent between the β1 and β2 receptors.
Chemical modification of the RTEM‐1 thiol β‐lactamase by thiol‐selective reagents: Evidence for activation of the primary nucleophile of the β‐lactamase active site by adjacent functional groups
Authors: Knap Anna K. , Pratt R. F. 
Published: May 2005

AbstractThe RTEM‐1 thiol β‐lactamase (Sigal, I. S., Harwood, B. G., Arentzen, R., Proc. Natl. Acad. Sci. USA. 79:7157–7160, 1982) is inactivated by thiol‐selective reagents such as iodoacetamide, methyl methanethiosulfonate, and 4,4′‐dipyridyldisulfide, which modify the active site thiol group. The pH‐rate profiles of these inactivation reactions show that there are two nucleophilic forms of the enzyme, EH2 and EH, both of which, by analogy with the situation with cysteine proteinases, probably contain the active site nucleophile in the thiolate form. The pKa of the active site thiol is therefore shown by the data to be below 4.0. This low pKa is thought to reflect the presence of adjacent functionality which stabilizes the thiolate anion. The low nucleophilicity of the thiolate in both EH2 and EH, with respect to that of cysteine proteinases and model compounds, suggests that the thiolate of the thiol β‐lactamase is stabilized by two hydrogen‐bond donors. One of these, of pKa greater than 9.0, is suggested to be the conserved and essential Lys‐73 ammonium group, of pKa around 6.7, is less clear, but may be the conserved Glu‐166 carboxylic acid. β‐Lactamase activity is associated with the EH2 form, and thus the β‐lactamase active site is proposed to contain one basic or nucleophilic group (the thiolate in the thiol β‐lactamase) and two acidic (hydrogen‐bond donor) groups (one of which is likely to be the above‐mentioned lysine ammonium group).
Use of restrained molecular dynamics in water to determine three‐dimensional protein structure: Prediction of the three‐dimensional structure of Ecballium elaterium trypsin inhibitor II
Authors: Chiche Laurent , Gaboriaud Christine , Heitz Annie , Mornon Jean‐Paul , Castro Bertrand , Kollman Peter A. 
Published: May 2005

AbstractRefinement of distance geometry (DG) structures of EETI‐II (Heitz et al.:Biochemistry 28:2392–2398, 1989), a member of the squash family trypsin inhibitor, have been carried out by restrained molecular dynamics (RMD) in water. The resulting models show better side chain apolar/polar surface ratio and estimated solvation free energy than structures refined “in cacuo.” The consistent lower values of residual NMR constraint violations, apolar/polar surface ration and solvation free energy of one of these refined structures allowed prediction of the 3D folding and disulfide connectivity of EETI‐II. Except for the few first residues for which no NMR constraints were available, this computer model fully agree with X‐ray structures of CMTI‐I (Boe et al.: FEBS Lett. 242:285–292, 1989) and EETI‐II complexed with trypsin that appeared after the RMD simulation was completed. Restrained molecular dynamics n water is thus proved to highly valuable for refinement of DG structures Also, the successful use of apolar/polar surface ratio and solvation free energy reinforce the analysis of Novotny et al. (Proteins 4: 19–30, 1988) and shows that these criteria are useful indicators of correct versus misfolded models.
Role of phosphorylation in conformational adaptability of bovine myelin basic protein
Authors: Deibler Gladys E. , Stone Audrey L. , Kies Marian W. 
Published: May 2005

AbstractControlled thrombic digestion of a preparation of components 2 + 3 isolated from the 18.5 kDa bovine myelin basic protein (MBP) yielded a polypeptide that was monophosphorylated on threonine 97 (component 3pT97). This is the first posttranslationally phosphorylated MBP isolated in pure form. We studied the effect of this single phosphate on the conformational adaptability of 18.5 kDa bovine MBP by comparing the circular dichroism (CD) spectrum of component 3pT97 with the spectra of highly purified nonphosphorylated components 1 and 2. The CD spectra of nonphosphorylated component 1 and component 2 [monodeamidated forms(s) of component1] were indistinguishable, while component 3pt97 exhibited a different spectrum. The singly phophorylated MBP component exhibited 13% more ordered conformations than that adopted by nonphosphorylated MBP in dilute aqueous solutions. This was estimated from the CD spectra, and apparently involved about 17 additional amino acid residues in β‐structure(s).
Apolar peptide models for conformational heterogeneity, hydration, and packing of polypeptide helices: Crystal structure of hepta‐ and octapeptides containing α‐aminoisobutyric acid
Authors: Karle Isabella L. , Flippen‐Anderson Judith L. , Uma K. , Balaram P. 
Published: May 2005

AbstractThe crystal structures of two helical peptides Boc‐Val‐Ala‐Leu‐Aib‐Val‐Ala‐Leu‐OMe (VALU‐7) and Boc‐Val‐Ala‐Leu‐Aib‐Val‐Ala‐Leu‐Aib‐OMe (VALU‐8) have been determined to a resolution of 1.0 and 0.9 Å, respectively. Both the seven and eight residue peptides crystallize with two conformers per asymmetric unit. The VALU‐8 conformers are completely helical and differ only at the C‐terminus by a sign reversal of the ϕ, ψ angles of the last residue. One of the VALUE‐7 conformers occurs as a normal α‐helix, whereas in the other, the N(7)O(3) α‐type hydrogen bond is ruptured by the entry of a water molecule (W) into the helix, which in turn makes hydrogen bonds N(7) ⃛W = 2.97 Å and ⃛O(3) = 2.77 Å. The other side of the water molecule is surrounded by a hydrophobic pocket. These two conformers give a static representation of a step in a possible helix unwinding or folding process. In the value‐8 crystal the helices aggregate in a parallel mode, whereas the aggregation is antiparallel in the VALU‐7 crystal. The crystal parameters are VALUE‐7 crystal. The crystal parameters are VALUE‐7, P21, a = 10.203 (3) Å, b = 19.744 (6) Å, c = 22.561 (6) Å, α = 96.76°, Z = 4, C38, H69N7O10·0.5 H2O, R = 6.65% for 3674 reflections observed >3σ(F): and VALU‐8, P21, a; = 10.596 (4) Å, b = 27.57 (6) Å, c = 17.745 (5) Å, β = 95.76 (3)°, Z = 4, C42H76N76O11·0.25 CH3OH, R = 6.63% for 4701 reflections observed >3σ(F).
Evaluation of homology modeling of HIV Protease
Authors: Weber Irene T. 
Published: May 2005

AbstractThe model of human immuno‐deficiency virus (HIV‐1) protease which was based on the crystal structure of Rous sarcoma virus (RSV) protease has been compared to the recently determined crystal structure of chemically synthesized HIV‐1 protease. The overall difference between the model and crystal structure was 1.4 Å root mean square (rms) deviation for 86 superimposed Cα atoms. The position of the flexible flap differs in the model and six residues at the amino terminus were incorrectly placed. With these exceptions, all atoms of the model and crystal structure agree to 2.11 Å runs deviation. The conformation of some surface bends in the model agrees less well with the crystal structure. Identical amino acids in RSV and HIV proteases were modeled more reliably than different types of amino acids. The amino acids which form the substrate binding site were modeled most accurately to 1.2 Å rms deviation for all atoms compared to the crystal structure. This suggests that functionally significant regions of related proteins can be modeled with high accuracy. The model gave correct predictions for residues making interactions with the substrate, and thereof could be used to design inhibitors, The model based on the RSV protease structure is more similar to the experimental structure than are previous models based on the structures of non‐viral aspartic proteases.
Solution structure of a zinc finger domain of yeast ADR1
Authors: Klevit Rachel E. , Herriott Jon R. , Horvarth Suzanna J. 
Published: May 2005

AbstractThe “zinc finger” is a 30‐residue repeating motif that has been identified in a variety of eukaryotic transcription factors. Each domain is capable of binding a Zn2+ ion through invariant Cys and His residues. We have determined the three‐dimensional structure of a synthetic peptide that corresponds to one of the two zinc finger domains in the yeast transcription factor ADR1, using two‐dimensional nuclear magnetic resonance spectroscopy. The Zn2+ ‐bound structure of the peptide consists of a loop containing the two Cys residues, a “fingertip,” a 12‐ to 13‐residue α‐helix containing the two His residues, and a C‐terminal tail. A majority of the interrresidue contacts observed invlove the seven conserved residues of the prototypic zinc finger (i.e., four zinc ligands and the three hydrophobic residues), indicating that these residues are largely responsible for the three‐dimensional structure of the domain and that all the zinc finger domains of the TFIIIA class will have similar structures, with the highest concentration of such residues on the external face of the α‐helix.
ALMA, an editor for large sequence alignments
Authors: Thirup Soren , Larsen Niels E. 
Published: May 2005

AbstractA dedicated sequence editor ALMA, was developed for aligning many sequences of proteins or RNA molecules or longer DNA fragments. Like previously published editors, ALMA is menu directed, screen oriented, and offers similarity and consensus display. ALMA has the additional features of collective movement of sequences, acceptance of input from many sources including structure files and databases, secondary structure display, and easy merging of alignments. In order to maintain sequence integrity and save disk space, gaps and sequences are stored separately. Automatic recovery of a session is possible. Finally, The program allows interaction between manual and automatic alignment.
Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis
Authors: Henrissat Bernard , Saloheimo Markku , Lavaitte Stéphane , Knowles Jonathan K. C. 
Published: May 2005

AbstractA number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.
Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
Authors: Gibrat Jean‐François , Gō Nobuhiro 
Published: May 2005

AbstractA normal mode analysis of human lysozyme has been carried out at room temperature. Human lysozyme is an enzyme constituted of two domains separated by an active site cleft, the motion of which is thought to be relevant for biological function. This motion has been described as a hinge bending motion. McCammon et al.1 have determined the characteristics of the hinge bending motion but they assumed a prior knowledge of the hinge axis. In this work we propose a method which is free from this assumption and determines the hinge axis and root mean square (rms) rotation angle which give the best agreement with the pattern of changes in all the distances between nonhydrogen atoms in the two domains, obtained by the normal mode analysis. The hinge axis we found is notably different from the one previously determined and goes, roughly, through the Cα 55 and Cα 76, i.e., it is located at the base of the β‐sheet of the second domain. The rms value for the rotation angle is also twice as large as the previous one: 3.37°. It is shown that this hinge bending motion provides a fairly good approximation of the dynamics of human lysozyme and that the normal mode with the lowest frequency has a dominating contribution to this hinge bending motion.A study of the accessible surface area of the residues within the cleft reveals that the motion does not result in a better exposure to the solvent of these residues.A characterization of the thermally excited state (under the hypothesis of the harmonicity of the potential energy surface) has been done using the concept of topology of atom packing. Under this hypothesis the thermal fluctuations result only in a small change of the topology of atom packing, leading therefore to nearly elastic deformations of the protein.
Design of biologically active, conformationally constrained GnRH antagonists
Authors: Struthers R. Scott , Tanaka Genzo , Koerber Steven C. , Solmajer Tom , Baniak Edmund L. , Gierasch Lila M. , Vale Wylie , Rivier Jean , Hagler Arnold T. 
Published: May 2005

AbstractThe introduction of conformational constraints into a flexible peptide hormone can be exploited to develop models for the conformation required for receptor binding and activity. In this review, we illustrate this approach to analog design using our work on antagonists of gonadotropin‐releasing hormone (GnRH). Design of a conformationally constrained, competitive antagonist of GnRH, cyclo[Δ3,4 Pro‐D4ClPhe‐DTrp‐Ser‐Tyr‐DTrp‐NMeLeu‐Arg‐Pro‐βAla], led to the prediction of its bioactive conformation. Template forcing experiments show that this conformation is accessible to other active GnRH analogs. Two‐dimensional NMR studies verified the predicted conformation in solution. The predicted binding conformation has recently been used to design two new analogs incorporating side chain–side chain linkages suggested by the conformational model:
These analogs were synthesized and the one predicted to be most similar to the parent conformation had equivalent potency while the second, designed to refine the conformational hypothesis, was found to exhibit enhanced potency, thus confirming the original binding conformation hypothesis. These compounds and their derivatives now provide a new class of GnRH antagonists possessing both high biological potency and limited conformational flexibility, thus making them ideal for both biophysical and structure–activity studies.
Hydrogen bonds involving sulfur atoms in proteins
Authors: Gregoret Lydia M. , Rader Stephen D. , Fletterick Robert J. , Cohen Fred E. 
Published: May 2005

AbstractIntrachain hydrogen bonds are a hallmark of globular proteins. Traditionally, these involve oxygen and nitrogen atoms. The electronic structure of sulfur is compatible with hydrogen bond formation as well. We surveyed a set of 85 high‐resolution protein structures in order to evaluate the prevalence and geometry of sulfur‐containing hydrogen bonds. This information should be of interest to experimentalists and theoreticians intersted in protein structure and protein engineering.
The frequency of ion‐pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions
Authors: Bryant Stephen H. , Lawrence Charles E. 
Published: May 2005

AbstractA statistical analysis of ion pairs in protein crystal structures shows that their abundance with respect to uncharged controls is accurately predicted by a Botlzmann‐like function of electrostatic potential. It appears that the mechanisms of protein folding and/or evolution combine to produce a “thermal” distribution of local nonbonded interactions, as has been suggested by statistical–mechanical theories. Using this relationship, we develop a maximum likelihood methodology for estimation of apparent energetic parameters from the data base of known structures, and we derive electrostatic potential functions that lead to optimal agreement of observed and predicted ion‐pair frequencies. These are similar to potentials of mean force derived from electrostatic theory, but departure from Coulombic behavior is less than has been suggested.
Single‐stranded DNA binding proteins (SSBs) from prokaryotic transmissible plasmids
Authors: Ruvolo Peter P. , Keating Kathleen M. , Williams Kenneth R. , Chase John W. 
Published: May 2005

AbstractThe DNA and protein sequences of single‐stranded DNA binding proteins (SSBs) encoded by the plP71a, plP231a, and R64 conjugative plasmids have been determined and compared to Escherichia coli SSB and the SSB encoded by F‐plasmid. Although the amino acid sequences of all of these proteins are highly conserved within the NH2‐terminal two‐thirds of the protein, they diverge in the COOH‐terminal third region. A number of amino acid residues which have previously been implicated as being either directly or indirectly involved in DNA binding are conserved in all of these SSBs. These residues include Trp‐40, Trp‐54, Trp‐88, His‐55, and Phe‐60. On the basis of these sequence comparisons and DNA binding studies, a role for Tyr‐70 in DNA binding is suggested for the first time. Although the COOH‐terminal third of these proteins diverges more than their NH2‐terminal regions, the COOH‐terminal five amino acid residues of all five of these proteins are identical. In addition, all of these proteins share the characteristic property of having a protease resistant, NH2‐terminal core and an acidic COOH‐terminal region. Despite the high degree of sequence homology among the plasmid SSB proteins, the F‐plasmid SSB appears unique in that it was the only SSB tested that neither bound well to poly(dA) nor was able to stimulate DNA polymerase III holoenzyme elongation rates. Poly [d(A‐T)] melting studies suggest that at least three of the plasmid encoded SSBs are better helix‐destabilizing proteins than is the E. coli SSB protein.
Comparison of the crystal structure of bacteriophage T4 lysozyme at low, medium, and high ionic strengths
Authors: Bell Jeffrey A. , Wilson Keith P. , Zhang Xue‐Jun , Faber Howard R. , Nicholson Hale , Matthews Brian W. 
Published: May 2005

AbstractCrystals of bacteriophage T4 lysozyme used for structural studies are routinely grown from concentrated phosphate solutions. It has been found that crystals in the same space group can also be grown from solutions containing 0.05 M imidazole chloride, 0.4 M sodium choride, and 30% polyethylene glycol 3500. These crystals, in addition, can also be equilibrated with a similar mother liquor in which the sodium chloride concentration is reduced to 0.025 M. The availability of these three crystal variants has permitted the structure of T4 lysozyme to be compared at low, medium, and high ionic strength. At the same time the X‐ray structure of phage T4 lysozyme crystallized from phosphate solutions has been further refined against a new and improved X‐ray diffraction data set.The structures of T4 lysozyme in the crystals grown with polyethylene glycol as a precipitant, regardless of the sodium chloride concentration, were very similar to the structure in crystals grown from concentrated phosphate solutions. The main differences are related to the formation of mixed disulfides between cysteine residues 54 and 97 and 2‐mercaptoethanol, rather than to the differences in the salt concentration in the crystal mother liquor. Formation of the mixed disulfide at residue 54 resulted in the displacement of Arg‐52 and the disruption of the salt bridge between this residue and Glu‐62.Other than this change, no obvious alterations in existing salt bridges in T4 lysozyme were observed. Neither did the reduction in the ionic strength of the mother liquor result in the formation of new salt bridge interactions. These results are consistent with the ideas that a crystal structure determined at high salt concentrations is a good representation of the structure at lower ionic strengths, and that models of electrostatic interactions in proteins that are based on crystal structures determined at high salt concentrations are likely to be relevant at physiological ionic strengths.
Computational studies of ligand diffusion in globins: I. Leghemoglobin
Authors: Czerminski Ryszard , Elber Ron 
Published: May 2005

AbstractThe thermally assisted diffusion of a small ligand (carbon monoxide) through a protein matrix (lupine leghemoglobin) is investigated computationally. The diffusion paths are calculated by a varient of the time‐dependent Hartree approximation which we call LES (locally enhanced sampling). The variant which was recently introduced by Elber and Karplus1 is based on the classical TD‐SCF approximation of Gerber et al.2 The simulation enables more significant search for diffusion pathways than was possible before. This is done by increasing the number of ligand trajectories using a single trajectory for the protein. We compare qualitatively diffusion rates in leghemoglobin and in myoglobin. The calculation shows that the diffusion in leghemoglobin is much faster than the diffusion in myoglobin, in agreement with experiment. The gate in leghemoglobin is opened by fluctuations at a close contact between the B/C and the G helices. The most relevant fluctuation is the rigid shift of the C helix with respect to the G helix. This path is not observed in a comparable calculation for myoglobin.1 This finding is rationalized by the lack of the D helix in leghemoglobin and a significantly more flexible CE loop. Supporting experimental evidence for the importance of the CE loop in leghemoglobin can be found in the kinetics studies of Gibson et al.28
Side chain–backbone hydrogen bonding contributes to helix stability in peptides derived from an α‐helical region of carboxypeptidase A
Authors: Bruch Martha D. , Dhingra Madan M. , Gierasch Lila M. 
Published: May 2005

AbstractRecently, Presta and Rose proposed1 that a necessary condition for helix formation is the presence of residues at the N‐and C‐termini (called NTBs and CTBs) whose side chains can form hydrogen bonds with the initial four amides and the last four carbonyls of the helix, which otherwise lack intrahelical hydrogen bonding partners. We have tested this hypothesis by conformational analysis by circular dichroism (CD) of a synthetic peptide corresponding to a region (171–188) of the protein carboxypeptidase A; in the protein, residues 174 to 186 are helical and are flanked by NTBs and CTBs. Since helix formation in this peptide may also be stabilized by electrostatic interactions, we have compared the helical content of the native peptide with that of several modified peptides designed to enable dissection of different contributions to helix stability. As expected, helix dipole interactions appear to contribute substantially, but we conclude that hydrogen bonding interactions as proposed by Presta and Rose also stabilize helix formation. To assist in comparison of different peptides, we have introduced two concentration‐independent CD parameters which are sensitive probes of helix formation.