bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the functional interplay between the primary site and the subsite of RNase T1: Kinetic analysis of single and multiple mutants for modified substrates
Authors: Steyaert Jan , Haikal Abdel Fattah , Wyns Lode 
Published: May 2005

AbstractWe report on the functional cooperativity of the primary site and the sub‐site of ribonuclease T1 (RNase T1; EC 3.1.27.3). The kinetic properties of the single Tyr‐38‐Phe and Asn‐98‐Ala mutants have been compared with those of the corresponding double mutant. The Tyr‐38‐Phe mutation has been used to probe enzyme‐substrate interactions at the primary site; the Asn‐98‐Ala mutation monitors subsite interactions.1 In addition to the dinucleoside phosphate substrate GpC, we measured the kinetics for GpMe, a synthetic substrate in which the leaving nucleoside cytosine has been replaced by methanol. All data were combined in a triple mutant box to analyze the interplay between Tyr‐38, Asn‐98, and the leaving group. The free energy barriers to kcat, introduced by the single Tyr‐38‐Phe and Asn‐98‐Ala mutations are not additive in the corresponding double mutant. The energetic coupling between both mutations is independent of the binding of the leaving cytosine at the subsite. We conclude that the coupling of the Tyr‐38‐Phe and Asn‐98‐Ala mutations arises through distortion or reorientation of the 3′‐guanylic acid moiety bound at the primary site. The experimental data indicate that the enzyme–substrate interactions beyond the scissile phosphodiester bond contribute to catalysis through the formation of new or improved contacts in going from ground state to transition state, which are functionally independent of primary site interactions. © 1994 John Wiley & Sons, Inc.
Analysis of Cα geometry in protein structures
Authors: Oldfield T. J. , Hubbard R. E. 
Published: May 2005

AbstractThe polypeptide of a protein molecule can be considered as a chain of Cα atoms linked by pseudobonds between the Cα atoms of successive amino acid residues. This paper presents an analysis of the angle and dihedral angles made by these pseudobonds in protein structures determined at high resolution by X‐ray crystallography. This analysis reveals a strong correlation between Cα geometry and the protein fold. The regular features of protein secondary structure such as α‐helix and α‐sheet are very clearly defined. In addition, it is possible to identify with some confidence the discrete populations of particular conformations of α‐turn. Comparison with the traditional Ramachandran type of plot demonstrates that an analysis of protein structure on the basis of Cα geometry provides a richer description of protein conformation. In addition, the characteristics of this geometry could be a useful guide in model building of protein structure. © 1994 John Wiley & Sons, Inc.
Structural basis for type I and type II deficiencies of antithrombotic plasma protein C: Patterns revealed by three‐dimensional molecular modelling of mutations of the protease domain
Authors: Greengard Judith S. , Fisher Cindy L. , Villoutreix Bruno , Griffin John H. 
Published: May 2005

AbstractFamilial deficiency of protein C is associated with inherited thrombophilia. To explore how specific missense mutations might cause observed clinical phenotypes, known protein C missense mutations were mapped onto three‐dimensional homology models of the protein C protease domain, and the implications for domain folding and structure were evaluated. Most Type I missense mutations either replaced internal hydrophobic residues (I201T, L223F, A259V, A267T, A346T, A346V, G376D) or nearby interacting residues (I403M, T298M, Q184H), thus disrupting the packing of internal hydrophobic side chains, or changed hydrophilic residues, thus disrupting ion pairs (N256D, R178W). Mutations (P168L, R169W) at the activation site destabilized the region containing the activation peptide structure. Most Type II mutations involved solvent‐exposed residues and were clustered either in a positively charged region (R147W, R157Q, R229Q, R352W) or were located in or near the active site region (S252N, D359N, G381S, G391S, H211Q). The cluster of arginines 147, 157, 229, and 352 may identify a functionally important exosite. Identification of the spatial relationships of natural mutations in the protein C model is helpful for understanding manifestations of protein C deficiency and for identification of novel, functionally important molecular features and exosites. © 1994 John Wiley & Sons, Inc.
Ion pair formation involving methylated lysine side chains: A theoretical study
Authors: Mavri Janez , Vogel Hans J. 
Published: May 2005

AbstractLysine residues with one, two, or three methyl groups substituted on the ϵ‐nitrogen atom are found in many proteins. To evaluate the effect of the posttranslational methylation on ion‐pair formation we have performed semiempirical and ab initio molecular orbital calculations, using the AMI method and the 6‐31G* basis set, respectively. Combinations of various methylated forms of methylamine and ethylamine with formate, acetate, and dimethyl phosphate were studied as model compounds. This approach allowed us to obtain information relevant to the interaction of the modified Lys residues with carboxylate groups of proteins, and the backbone of nucleic acids. We have found that the interaction energy decreases with an increasing number of methyl groups. Inclusion of a solvent reaction field in the semiempirical calculations gave reasonable values for the interaction energy in aqueous solution, when formate and acetate were the counterions. These studies suggest that, in addition to other factors, a weakening of ionic interactions contributes to the various physiological effects of lysine methylation. © 1994 John Wiley & Sons, Inc.
Structure of trichosanthin at 1.88 Å resolution
Authors: Zhou Kangjing , Fu Zhuji , Chen Minghuang , Lin Yujuan , Pan Kezhen 
Published: May 2005

AbstractTrichosanthin (TCS) is one of the single chain ribosome‐inactivating proteins (RIPs). The crystals of the orthorhombic form of trichosanthin have been obtained from a citrate buffer (pH 5.4) with KC1 as the precipitant. The crystal belongs to the space group P212121 with a = 38.31, b = 76.22, c = 79.21 Å. The structure was solved by molecular replacement method and refined using the programs XPLOR and PROLSQ to an R‐factor of 0.191 for the reflections within the 6–1.88 Å resolution range. The bond length and bond angle in the protein molecule have root‐mean‐square deviations from ideal value of 0.013 Å and 3.3°, respectively. The refined model includes 247 residues and 197 water molecules. The TCS molecule consists of two structural domains. The large domain contains six α‐helices, a six stranded sheet, and an antiparallel β‐sheet. The small domain has a largest α‐helix, which shows a distinct bend. The possible active site of the molecule located on the cleft between two domains was proposed. In the active site Arg‐163 and Glu‐160, Glu‐189 and Arg‐122 form two ion pairs, Glu‐189 and Gln‐156 are hydrogen bonded to each other. Three water molecules are bonded to the residues in the active site region. The structures of TCS molecule and ricin A‐chain (RTA) superimpose quite well, showing that the structures of the two protein molecules are homologous. Comparison of the structures of the TCS molecule in this orthorhombic crystal with that in the monoclinic crystal indicates that there are no essential differences of the structures between the two protein crystals. © 1994 Wiley‐Liss, Inc.
Helix‐forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing
Authors: Okamoto Yuko 
Published: May 2005

AbstractMonte Carlo simulated annealing is applied to the study of the α‐helix‐forming tendencies of seven nonpolar amino acids, Ala, Leu, Met, Phe, Ile, Val, and Gly. Homooligomers of 10 amino acids are used and the helix tendency is calculated by folding α‐helicies from completely random initial conformations. The results of the simulation imply that Met, Ala, and Leu are helix formers and that Val, Ile, and Gly are helix breakers, while Phe comes in between the two groups. The differences between helix formers and breakers turned out to be large in agreement with the recent experiments with short peptides. It is argued from the energy distributions of the obtained conformations that the helix tendency is small for the helix breakers because of steric hindrance of side chains. Homoglycine is shown to favor a random coil conformation. The β‐strand tendencies of the same homooligomers are also considered, and they are shown to agree with the frequencies of amino acids in β‐sheet from the protein data base. © 1994 Wiley‐Liss, Inc.
Temperature‐induced complementarity as a mechanism for biomolecular assembly
Authors: Leikin S. , Parsegian V. A. 
Published: May 2005

AbstractRecent advances in the measurement and theory of “hydration” interactions between biomolecules provide a basis on which to formulate mechanisms of biomolecular recognition. In this paper we have developed a mathematical formalism for analyzing specificity encoded in dynamic distributions of surface polar groups, a formalism that incorporates newly recognized properties of directly measured “hydration” forces. As expected, attraction between surfaces requires complementary patterns of surface polar groups. In contrast to usual expectations, thermal motion can create these complementary surface configurations. We have demonstrated that assembly can occur with an increase in conformational entropy of polar residues. Elevated temperature then facilitates recognition rather than hinders it. This mechanism might underlie some temperature‐favored assembly reactions common in biological systems that are usually associated with the “hydrophobic effect” only. © 1994 Wiley‐Liss, Inc.
Kinetic study on myoglobin refolding monitored by five optical probe stopped‐flow methods
Authors: Chiba Kaori , Ikai Atsushi , Kawamura‐Konishi Yasuko , Kihara Hiroshi 
Published: May 2005

AbstractThe refolding kinetics of horse cyanometmyoglobin induced by concentration jump of urea was investigated by five optical probe stopped‐flow methods: absorption at 422 nm, tryptophyl fluorescence at around 340 nm, circular dichroism (CD) at 222 nm, CD at 260 nm, and CD at 422 nm. In the refolding process, we detected three phases with rate constants of > 1 × 102 s−1, (4.5–9.3) S−1, and (2–5) × 10−3 s−1. In the fastest phase, a substantial amount of secondary structure (40%) is formed within the dead time of the CD stopped‐flow apparatus (10.7 ms). The kinetic intermediate populated in the fastest phase is shown to capture a hemindicyanide, suggesting that a “heme pocket precursor” recognized by hemindicyanide must be constructed within the dead time. In the middle phase, most of secondary and tertiary structures, especially around the captured hemindicyanide, have been constructed. In the slowest phase, we detected a minor structural rearrangement accompanying the ligand‐exchange reaction in the fifth coordination of ferric iron. We present a possible model for the refolding process of myoglobin in the presence of the heme group. © 1994 Wiley‐Liss, Inc.
Decoupling of melting domains in immobilized ribonuclease A
Authors: Rialdi Giovanni , Battistel Ezio 
Published: May 2005

AbstractRibonuclease A has been immobilized on silica beads through glutaraldeyde‐mediated chemical coupling in order to improve the stability of the protein against thermal denaturation. The thermodynamic and binding properties of the immobilized enzyme have been studied and compared with those of the free enzyme. The parameters describing the binding of the inhibitor 3′ ‐CMP (Ka and ΔH) as monitored by spectrophotometry and calorimetry were not significantly affected after immobilization. Conversely both the stability and unfolding mechanism drastically changed. Thermodynamic analysis of the DSC data suggests that uncoupling of protein domains has occurred as a consequence of the immobilization. The two state approximation of the protein unfolding process is not longer valid for the immobilized RNase. Protein stability strongly depends on the hydrophobicity properties of the support surface as well as on the presence of the inhibitor and pH. For example, after immobilization on a highly hydrophobic surface, the enzyme is partially in the unfolded state. The binding of a ligand is able to reorganize the protein structure into a native‐like conformation. The refolding rates are different for the two protein domains and vary as a function of pH and presence of the inhibitor 3′‐CMP. © 1994 Wiley‐Liss, Inc.
Characterization of two crystal forms of Clostridium thermocellum endoglucanase CelC
Authors: Dominguez Roberto , Souchon Hélène , Alzari Pedro M. 
Published: May 2005

AbstractEndoglucanase CelC from Clostridium thermocellum expressed in Escherichia coli has been crystallized in two different crystal forms by the hanging drop method. Crystals of form I were grown with polyethylene glycol as a precipitant. They are orthorhombic, space group P212121, with cell dimensions a =51.4 Å, b =84.3 Å, and c =87.5 Å. Crystals of form II, obtained in ammonium sulfate solutions, belong to the tetragonal space group P41212 (or P43212) with cell dimensions of a = b = 130.7 Å and c = 69.6 Å. Diffraction data to 2.8 Å resolution were observed for both crystal forms with a rotating anode generator. Preliminary oscillation images of the orthorhombic form I crystals using a synchrotron radiation source show diffraction to 2.2 Å resolution, indicating that these crystals are suitable for high resolution crystallographic analysis. © 1994 Wiley‐Liss, Inc.
Crystallization of an enzyme‐inhibitor complex: Proteinase K with its protein inhibitor, PK13
Authors: Pal Gour P. , Jany Klaus D. , Tsernoglou Demetrius 
Published: May 2005

AbstractCrystals of a complex of proteinase K (molecular mass, 28,790 Da) with its naturally occurring protein inhibitor PK13 (19,641 Da), have been prepared by a microdialysis technique and modified by hanging drop vapor diffusion against 25% ammonium sulfate in 50 mM Tris‐HCl, pH 7.8. The crystals are long prisms with diamond‐shaped cross sections of 0.2 × 0.4 × 1.5 mm3 and they diffract X‐rays to a resolution of 2.5 Å. They belong to the orthorhombic space group P212121 with cell dimensions a = 64.1 Å, b = 66.8 Å, and c = 133.8 Å. Assuming one whole complex in the asymmetric unit, one obtains VM = 2.95 Å3/Da and the solvent content, Vsolv = 58.3%. © 1994 Wiley‐Liss, Inc.
Searching protein structure databases has come of age
Authors: Holm Liisa , Sander Chris 
Published: May 2005

AbstractThe number of protein structures known in atomic detail has increased from one in 1960 (Kendrew, J. C., Strandberg, B. E., Hart, R. G., Davies, D. R., Phillips, D. C., Shore, V. C. Nature (London) 185:422–427, 1960) to more than 1000 in 1994. The rate at which new structures are being published exceeds one a day as a result of recent advances in protein engineering, crystallography, and spectroscopy. More and more frequently, a newly determined structure is similar in fold to a known one, even when no sequence similarity is detectable. A new generation of computer algorithms has now been developed that allows routine comparison of a protein structure with the database of all known structures. Such structure database searches are already used daily and they are beginning to rival sequence database searches as a tool for discovering biologically interesting relationships. © 1994 Wiley‐Liss, Inc.
HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
Authors: Eisen Michael B. , Wiley Don C. , Karplus Martin , Hubbard Roderick E. 
Published: May 2005

AbstractA program (HOOK) is described for generating potential ligands that satisfy the chemical and steric requirements of the binding region of a macromolecule. Functional group sites with defined positions and orientations are derived from known ligand structures or the multicopy simulation search (MCSS) method (Miranker, A., Karplus, M. Proteins 11:29–34, 1991). HOOK places molecular “skeletons” from a database into the protein binding region by making bonds between sites (“hooks”) on the skeleton and functional groups. The nonpolar interactions with the binding region of candidate molecules are assessed by use of a simplified van der Waals potential. The method is illustrated by constructing ligands for the sialic acid binding site of the hemagglutinin from the influenza A virus and the active site of chloramphenicol acetyltransferase. Aspects of the HOOK program that lead to a highly efficient search of 105 or more skeletons for binding to 102 or more functional group minima are outlined. © 1994 Wiley‐Liss, Inc.
Parser for protein folding units
Authors: Holm Liisa , Sander Chris 
Published: May 2005

AbstractGeneral patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X‐ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and minimal interaction between units (domains). In a simple harmonic approximation, interdomain dynamics is determined by the strength of the interface and the distribution of masses. The most likely domain decomposition involves units with the most correlated motion, or largest interdomain fluctuation time. The decomposition of a convoluted 3‐D structure is complicated by the possibility that the chain can cross over several times between units. Grouping the residues by solving an eigenvalue problem for the contact matrix reduces the problem to a one‐dimensional search for all reasonable trial bisections. Recursive bisection yields a tree of putative folding units. Simple physical criteria are used to identify units that could exist by themselves. The units so defined closely correspond to crystallographers' notion of structural domains. The results are useful for the analysis of folding principles, for modular protein design and for protein engineering. © 1994 Wiley‐Liss, Inc.
X‐ray crystal structure and molecular dynamics simulation of bovine pancreas phospholipase A2–n‐dodecylphosphorylcholine complex
Authors: Tomoo Koji , Ohishi Hirofumi , Ishida Toshimasa , Inoue Masatoshi , Ikeda Kiyoshi , Sumiya Shigeyuki , Kitamura Kunihiro 
Published: May 2005

AbstractThe crystal structure of n‐dodecylphosphorylcholine (n‐C12PC)–bovine pancreas phospholipase A2 (PLA2) complex provided the following structural.characteristics: (1) the dodecyl chain of n‐C12PC was located at the PLA2 N ‐terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2‐acyl fatty acid chain (β‐chain) of the substrate phospholipid, (2) the region from Lys‐53 to Lys‐56 creates a cholinereceiving pocket of n‐C12PC and (3) the N‐termillal group of Ala‐1 shifts significantly toward the Tyr‐52 OH group by the binding of the n‐C12PC inhibitor. Since the accuracy of the X‐ray analysis (R = 0.275 at 2.3 Å resolution) was insufficient to establish these important X‐ray insights, the complex structure was further investigated through the molecular dynamics (M D) simulation, assuming a system in aqueous solution at 310K. The M D simulation covering 176 ps showed that the structural characteristics observed by X‐ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the M D simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n‐C12PC hydrocarbon chain. © 1994 Wiley‐Liss, Inc. © 1994 Wiley‐Liss, Inc.
Structure and dynamics of the neutrophil defensins NP‐2, NP‐5, and HNP‐1: NMR studies of amide hydrogen exchange kinetics
Authors: Skalicky Jack J. , Selsted Michael E. , Pardi Arthur 
Published: May 2005

AbstractThe exchange kinetics for the slowly exchanging amide hydrogens in three defensins, rabbit NP‐2, rabbit NP‐5, and human HNP‐1, have been measured over a range of pH at 25°C using 1D and 2D NMR methods. These NHs have exchange rates 102 to 105 times slower than rates from unstructured model peptides. The observed distribution of exchange rates under these conditions can be rationalized by intramolecular hydrogen bonding of the individual NHs, solvent accessibility of the NHs, and local fluctuations in structure. The temperature dependencies of NH chemical shifts (NH temperature coefficients) were measured for the defensins and these values are consistent with the defensin structure. A comparison is made between NH exchange kinetics, NH solvent accessibility, and NH temperature coefficients of the defensins and other globular proteins. Titration of the histidine side chain in NP‐2 was examined and the results are mapped to the three‐dimensional structure. © 1994 Wiley‐Liss, Inc.
Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
Authors: Lee Kon Ho , Xie Dong , Freire Ernesto , Amzel L. Mario 
Published: May 2005

AbstractTheoretical estimations of changes in side chain configurational entropy are essential for understanding the different contributions to the overall thermodynamic behavior of important biological processes like folding and binding. The configurational entropy of any given side chain in any particular protein can be evaluated from the complete energy profile of the side chain. Calculations of the energy profiles can be performed using the side chain single bond dihedrals as the only independent variables as long as the structures at each value of the dihedrals are allowed to relax through small changes in the valence bond angles. The probabilities of different side chain conformers obtained from these energy profiles are very similar to the conformer populations obtained by analysis of side chain preferences in the proteins of the Protein Data Bank. Also, side chain conformational entropies obtained from the energy profiles agree extremely well with those obtained from the Protein Data Bank conformer populations. Changes in side chain configurational entropy in binding and folding can be computed as differences in conformational entropy because, in most cases, the frequency of the rotational oscillation around the energy minimum of any given conformer does not appear to change significantly in the reaction. Changes of side chain conformational entropy calculated in this way were compared with experimental values. The only available experimental data–the effect of side chain substitution on the stability of α‐helices–were used for this comparison. The experimental values were corrected to subtract the solvent contributions. This comparison yields an excellent agreement between calculated and experimental values, validating not only the theoretical estimates but also the separability of the entropic contributions into configurational terms and solvation related terms. © 1994 Wiley‐Liss, Inc.