bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space
Authors: Caflisch Amedeo , Niederer Peter , Anliker Max
Published: May 2005

A new minimization procedure for the global optimization is cartesian coordinate space of the conformational energy of a polypeptide chain is presented. The Metropolis Monte Carlo minimization is thereby supplemented by a thermalization process, which is initiated whenever a structure becomes trapped in an area containing closely located local minima in the conformational space. The method has been applied to the endogenous opioid pentapeptide methionine enkephalin. Five among 13 different starting conformations led to the same apparent global minimum of an in‐house developed energy function, a type II′ reverse turn, the central residues of which are Gly‐3‐Phe‐4. A comparison between the ECEPP/2 global minimum conformation of methionine enkephalin and the apparent one achieved by the present method shows that minimum‐energy conformations having a certain similarity can be generated by relatively different force fields. © 1992 Wiley‐Liss, Inc.
Overproduction, crystallization, and preliminary X‐ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB
Authors: Schindelin Hermann , Herrler Michael , Willimsky Gerald , Marahiel Mohamed A. , Heinemann Udo
Published: May 2005

The major co ld shock protein form Bacillus subtilis (CspB) was voerexressed using the bacteriophage T7 RNA polymerase/promotor system and purified to apparent homogeneity from recombinant Escherichia coli cells. CspB was crystallized in two different forms using vapor diffusion methods. The first crystal form obtained with ammonium sulfate as precipitant belongs to the trigonal crystal system, space group P3121 (P3221) with unit cell dimensions a = b = 59.1 Å and c = 46.4 Å. The second crystal form is tetragonal, space group P41212 (P43212) with unit cell dimensionsa = b = 56.9 Å and c = 53.0 Å. These crystals grow with polyethylene glycol 4000 as precipitant. © 1992 Wiley‐Liss, Inc.
The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor
Authors: Varghese Joseph N. , McKimm‐Breschkin Jennifer L. , Caldwell James B. , Kortt Alexander A. , Colman Peter M.
Published: May 2005

Crystallographic studies of neuraminidase–sialic acid complexes indicate that sialic acid is distorted on binding the enzyme. Three arginine residues on the enzyme interact with the carboxylate group of the sugar which is observed to be equatorial to the saccharide ring as a consequence of its distorted geometry. The glycosidic oxygen is positioned within hydrogen‐bonding distance of Asp‐151, implicating this residue in catalysis. © 1992 Wiley‐Liss, Inc.
Comparative molecular modeling and crystallization of P‐30 protein: A novel antitumor protein of Rana pipiens oocytes and early embryos
Authors: Mosimann Steven C. , Johns Kathy L. , Ardelt Wojciech , Mikulski Stanislaw M. , Shogen Kuslima , James Michael N. G.
Published: May 2005

The P‐30 protein (Onconase™)

Onconase™ is a trademark of Alfacell Corporation.

of Rana pipiens oocytes and early embryos is homologous to members of the pancreatic ribonuclease superfamily and exhibits an antitumor activity in vitro and in vivo. It appears that the ribonucleolytic activity of P‐30 protein may be required for its antitumor effects. A comparative molecular model of P‐30 protein has been constructed based upon the known three‐dimensional structure of bovine pancreatic RNase A in order to provide structural information. Functionally, these enzymes hydrolyze oligoribonucleotides to pyrimidine‐3′‐phosphate monoesters and 5′‐OH ribonucleotides. In the modeling procedure, automated sequence alignments were revised based upon the inspection of the RNase A structure before the amino acids of the P‐30 protein were assigned the coordinates of the RNase A template. The inevitable intermolecular steric clashes that result were relieved on an interactive graphics device through theadjustment of side chain torsion angles. This process was followed by energy minimization of the model, which served to optimize stereochemical geometry and to relieve any remaining unacceptably close contacts. The resulting model retains the essential features of RNase A as sequence insertions and deletions are almost exclusively found in exposed surface loops. The all atom superposition of active site residues of the P‐30 protein model and an identically minimized RNase A structure has a root mean square deviation of 0.52 Å. Though tentative, the model is consistent with a pyrimidine specificity. Further, the model suggests Lys9 (P‐30 protein) can donate a hydrogen bond to the active site phosphate, whereas it is unlikely that P‐30 protein binds the 3′‐ribonucleotide in a fashion similar to RNase A. P‐30 protein has been crystallized in an orthorhombic space group, P212121, with unit cell dimensions, a = 40.76, b = 69.77, and c = 32.54 Aring;. The crystals grow as small rosettes from an ammonium sulfate solution at pH 4.5. © 1992 Wiley‐Liss, Inc.
Generation of a substructure library for the description and classification of protein secondary structure. II. Application to spectra–structure correlations in fourier transform infrared spectroscopy
Authors: Prestrelski Steven J. , Byler D. Michael , Liebman Michael N.
Published: May 2005

Fourier transform infrared spectroscopy has become well known as a sensitive and informative tool for studying secondary structure in proteins. Present analysis of the conformation‐sensitive amide I region in protein infrared spectra, when combined with band narrowing techniques, provides more information concerning protein secondary structure than can be meaningfully interpreted. This is due in part to limited models for secondary structure. Using the algorithm described in the previous paper of this series, we have generated a library of substructures for several trypsin‐like serine proteases. This library was used as a basis for spectra–structure correlations with infrared spectra in the amide I′ region, for five homologous proteins for which spectra were collected. Use of the substructure library has allowed correlations not previously possible with template‐based methods of protein conformational analysis. © 1992 Wiley‐Liss, Inc.
Crystallization, sequence, and preliminary crystallographic data for an antipeptide Fab 50.1 and peptide complexes with the principal neutralizing determinant of HIV‐1 gpl20
Authors: Sturam Enrico A. , Stanfield Robyn L. , Fieser Gail G. , Silver Sandra , Roguska Michael , Hincapie L. Marina , Simmerman Heather K. B. , Profy Albert T. , Wilson Ian A.
Published: May 2005

X‐ray quality crystals of an Fab fragment from an antipeptide monoclonal antibody (R/V3‐50.1) that recognizes the principal neutralizing determinant (PND) of the gpl20 glycoprotein of human immunodeficiency virus type 1 (HIV‐1) (MN isolate) were grown as uncomplexed and peptide complexed forms. Crystals of the free Fab grew from high salt in orthorhombic space groups P212121 and I222 and from polyethylene glycol in space groups P1 and P21. Seeds from either the P1 and P21 native (uncomplexed) Fab crystals induced nucleation of crystals of the Fab complexed to a 16‐residue synthetic peptide corresponding to the PND when streak seeded into preequilibrated solutions of this complex. Data were collected from these complex crystals and from each of the four native Fab forms to at least 2.8Å resolution. The genes for the variable domain of the Fab were cloned and sequenced and the primary amino acid sequence was deduced from this information. Knowledge of the three‐dimensional structure of this Fab–pep‐tide complex will be important in the understanding of the PND of HIV‐1 and its recognition by neutralizing monoclonal antibodies. © 1992 Wiley‐Liss, Inc.
The quaternary structure of carbonmonoxy hemoglobin ypsilanti
Authors: Janin Joël , Wodak Shoshana J.
Published: May 2005

We present a geometric analysis of the allosteric interface in the new Y state quaternary structure observed in liganded mutant hemoglobin Ypsilanti (β99 Asp → Tyr) by Smith, F.R., Lattman, E.E., Carter, C.W., Jr. (Proteins 10:81–91, 1991). The classical T to R quaternary structure change being a rotation of αβ dimers about an axis which is approximately parallel to the dimer axis of pseudosym‐metry, the new quaternary structure is obtained by applying to R an additional rotation about an axis orthogonal to the first. This suggests that Y is a modified R state rather than an intermediate on the T to R pathway. Computer docking experiments designed to simulate the quaternary structure change support this suggestion. © 1993 Wiley‐Liss, Inc.
The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state
Authors: Tidor Bruce , Karplus Martin
Published: May 2005

The vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin‐reactive site. Favorable contributions to the free energy of 2.5–5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of crosslinks are discussed. © 1993 Wiley‐Liss, Inc.
Studies of the zein‐like α‐prolamins based on an analysis of amino acid sequences: Implications for their evolution and three‐dimensional structure
Authors: Garratt Richard , Oliva Glaucius , Caracelli Ignez , Leite Adilson , Arruda Paulo
Published: May 2005

α‐Prolamins are the major seed storage proteins of species of the grass tribe Andropogonea. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats presumed to be the result of multiple intragenic duplication. Two new sequences of α‐prolamin clones from Coix (pBCX25.12 and pBCX25.10) are compared with similar clones from maize and Sorghum in order to investigate evolutionary relationships between the repeat motifs and to propose a schematic model for their three‐dimensional structure based on hydrophobic membrane‐helix propensities and helical “wheels.” A scheme is proposed for the most recent events in the evolution of the central part of the molecule (repeats 3 to 8) which involves two partial intragenic duplications and in which contemporary odd‐numbered and even‐numbered repeats arise from common ancestors, respectively. Each pair of repeats is proposed to form an antiparallel α‐helical hairpin and that the helices of the molecule as a whole are arranged on a hexagonal net. The majority of helices show six faces of alternating hydrophobic and polar residues, which give rise to intersticial holes around each helix which alternate in chemical character. The model is consistent with proteins which contain different numbers of repeats, with oligomerization and with the dense packaging of α‐prolamins within the protein body of the seed endosperm. © 1993 Wiley‐Liss, Inc.
Crystal structure of CTP‐ligated T state aspartate transcarbamoylase at 2.5 Å resolution: Implications for ATCase mutants and the mechanism of negative cooperativity
Authors: Kosman Richard P. , Gouaux J. Eric , Lipscomb William N.
Published: May 2005

The X‐ray crystal structure of CTP‐ligated T state aspartate transcarbamoylase has been refined to an R factor of 0.182 at 2.5 Å resolution using the computer program X‐PLOR. The structure contains 81 sites for solvent and has rms deviations from ideality in bond lengths and bond angles of 0.018 Å and 3.722°, respectively. The cytosine base of CTP interacts with the main chain carbonyl oxygens of rTyr‐89 and rIle‐12, the main chain NH of rIle‐12, and the amino group of rLys‐60. The ribose hydroxyls form polar contacts with the amino group of rLys‐60, a carboxylate oxygen of rAsp‐19, and the main chain carbonyl oxygen of rVal‐9. The phosphate oxygens of CTP interact with the amino group of rLys‐94, the hydroxyl of rThr‐82, and an imidazole nitrogen of rHis‐20. Recent mutagenesis experiments evaluated in parallel with the structure reported here indicate that alterations in the hydrogen bonding environment of the side chain of rAsn‐111 may be responsible for the homotropic behavior of the pAR5 mutant of ATCase. The location of the first seven residues of the regulatory chain has been identified for the first time in a refined ATCase crystal structure, and the proximity of this portion of the regulatory chain to the allosteric site suggests a potential role for these residues in nucleotide binding to the enzyme. Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase. © 1993 Wiley‐Liss, Inc.
Purification, crystallization, and preliminary X‐ray studies on the rhizome lectin from stinging nettle and its complex with NN′N″‐triacetylchitotriose
Authors: Loris Remy , Thi Minh Hoa Dao , Lisgarten John , Wyns Lode
Published: May 2005

Single crystals were grown from affinity‐purified stinging nettle lectin and from its complex with the specific trisaccharide NN′N″ ‐triacetylchitotriose by vapor diffusion at room temperature. The lectin crystallizes in space group P212121 with unit cell dimensions a = 54.3 (1) Å, b = 62.2 (1) Å, and c = 92.4 (2) Å, and diffracts to 3.0 Å resolution. The asymmetric unit contains three lectin monomers. The crystals of the lectin‐trisaccharide complex have space group P212121 with cell constants a = 37.69 (4) Å, b = 48.97 (6) Å, and c = 57.32 (4) Å. These crystals diffract to at least 2.0 Å resolution and the asymmetric unit contains one lectin monomer. A three‐dimensional X‐ray structure determination is on its way. © 1993 Wiley‐Liss, Inc.
On the calculation of pKas in proteins
Authors: Yang An‐Suei , Gunner M. R. , Sampogna Rosemary , Sharp Kim , Honig Barry
Published: May 2005

This paper describes a general method to calculate the pKas of ionizable groups in proteins. Electrostatic calculations are carried out using the finite difference Poisson–Boltzmann (FDPB) method. A formal treatment of the calculation of pKas within the framework of the FDPB method is presented. The major change with respect to previous work is the specific incorporation of the complete charge distribution of both the neutral and charged forms of each ionizable group into the formalism. This is extremely important for the treatment of salt bridges. A hybrid statistical mechanical/Tanford–Roxby method, which is found to be significantly faster than previous treatments, is also introduced. This simplifies the problem of summing over the large number of possible ionization states for a complex polyion. Applications to BPTI and serine proteases suggest that the calculations can be quite reliable. However, the necessity of including bound waters in the treatment of the Asp‐70…His‐31 salt bridge in T4 lysozyme and experience with other proteins suggest that additional factors ultimately need to be considered in a comprehensive treatment of pKas in proteins. © 1993 Wiley‐Liss, Inc.
Multiple‐site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins
Authors: Gilson Michael K.
Published: May 2005

Computer models of proteins frequently treat the energies and forces associated with ionizable groups as if they were purely electrostatic. This paper examines the validity of the purely electrostatic approach, and concludes that significant errors in energies can result from the neglect of ionization changes. However, a complete treatment of ionizable groups presents substantial computational obstacles, because of the large number of ionization states which must be examined in systems having multiple interacting titratable groups. In order to address this problem, two novel methods for treating the energetics and forces associated with ionizable groups with a minimum of computer time have been developed. The most rapid method yields approximate energies by computing the free energy of a single highly occupied ionization state. The second method separates ionizable groups into clusters, and treats intracluster interactions exactly, but intercluster interactions approximately. This method yields both accurate energies and fractional charges. Good results are obtained in tests of both methods on proteins having has many as 123 ionizable groups. The more rapid method requires computer times of 0.01 to 0.34 sec, while the more accurate method requires 0.7 to 15 sec. These methods may be fast enough to permit the incorporation of ionization effects in iterative computations, such as energy minimizations and conformational searches. © 1993 Wiley‐Liss, Inc.
The structure of a thermally stable 3‐phosphoglycerate kinase and a comparison with its mesophilic equivalent
Authors: Davies Gideon J. , Gamblin Steven J. , Littlechild Jennifer A. , Watson Herman C.
Published: May 2005

The structure of the phosphoglycerate kinase (PGK) from Bacillus stearothermophilus, a moderate thermophile, has been determined and compared with that of its mesophilic equivalent from yeast. The Bacillus enzyme structure was solved by molecular replacement and improved using constrained rigid‐body, molecular dynamics and conventional refinement procedures. The refinement residual, calculated using all the measured data between 8 and 1.65 Å, is 0.18(1). The stereo chemical deviations of the final model from ideality are 0.01 Å for both bonds and planes.

The mid‐point temperatures of the Bacillus and yeast enzymes are 67 and 53°C, respectively. Differential scanning calorimetry indicates that the energy difference (ΔΔG) between the mesophilic and thermophilic enzymes is of the order of 5 kcal mol−1 at room temperature. The structure comparison indicates that the features most likely to be responsible for the increased thermal stability of the Bacillus enzyme are the increased internal hydrophobicity, additional ion pairs, and better α‐helix stability resulting from the removal of helix destablising residues and extra helix–dipole/helix side chain ionic interactions. © 1993 Wiley‐Liss, Inc.
Small effects of amino acid replacements on the reduced and unfolded state of pancreatic trypsin inhibitor
Authors: Goldenberg David P. , Zhang Jian‐Xin
Published: May 2005

The effects of amino acid replacements on the hydrodynamic volume of reduced and unfolded bovine pancreatic trypsin inhibitor (BPTI) have been examined by gel electrophoresis. The electrophoretic mobilities of the reduced forms of 46 BPTI variants were compared at room temperature in the absence of denaturants. The single substitutions examined include many different types of replacements at sites throughout the polypeptide, and, collectively, alter 22 of the 58 residues of the wild‐type protein. The only substitutions found to alter the electrophoretic mobility of the reduced protein by more than ∼3% are those that change the net charge of the protein. For nine mutants, the rates of disulfide formation in the reduced protein were also examined and found to be very similar to that of the wild‐type protein. These results suggest that any structure that may be present in the reduced protein is either relatively insensitive to amino acid replacements or does not greatly influence the averaged properties of the polypeptide chain. © 1993 Wiley‐Liss, Inc.
Theoretical studies of relaxation of a monomeric subunit of HIV‐1 protease in water using molecular dynamics
Authors: Venable Richard M. , Carson Frederick W. , Brooks Bernard R.
Published: May 2005

The dynamic behavior of one 99‐residue subunit of the dimeric aspartyl protease of HIV‐1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N‐ and C‐0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N‐terminus displayed the greatest fluctuational disorder whereas the C‐terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy‐atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV‐1 protease monomer than the subunit conformation seen in the X‐ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley‐Liss, Inc.
Computer simulation of antibody binding specificity
Authors: Pellegrini Matteo , Doniach Sebastian
Published: May 2005

A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse‐grained pair potentials. The final refinement of our best solutions using all‐atom OPLS potentials (Jorgensen and Tirado‐Rives8) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance‐dependent dielectric function is an improvement over the more commonly used linear form. © 1993 Wiley‐Liss, Inc.
Recombinant antineuraminidase single chain antibody: Expression, characterization, and crystallization in complex with antigen
Authors: Malby Robyn L. , Caldwell J. Bruce , Gruen L. Clem , Harley Vincent R. , Ivancic Neva , Kortt Alexander A. , Lilley Glenn G. , Power Barbara E. , Webster Robert G. , Colman Peter M. , Hudson Peter J.
Published: May 2005

The variable heavy (VH) and variable light (VL) genes of NC10, a monoclonal antibody with specificity toward N9 neuraminidase (NA), were cloned and sequenced. A single chain Fv (scFv) fragment of NC10, consisting of VH and VL domains joined by a peptide linker, was designed, constructed and expressed in the E. coli expression vector pPOW. The N‐terminal secretion signal PelB directed the synthesized protein into the periplasm where it was associated with the insoluble membrane fraction. An octapeptide (FLAG) tail was fused to the C‐terminus of the single chain Fv to aid in its detection and remained intact throughout the protein purification process. NC10 scFv was purified by solubilization of the E. coli membrane fraction with guanidinium hydrochloride followed by column chromatography. The purified NC10 scFv showed binding affinity for its antigen, NA, 2‐fold lower than that of the parent Fab. The complex between NA and the scFv has been crystallized by the vapor diffusion method. The crystals are tetragonal, space group P4212, with unit cell dimensions a = b = 141 Å, c = 218 Å. © 1993 Wiley‐Liss, Inc.
Surface motifs by a computer vision technique: Searches, detection, and implications for protein–ligand recognition
Authors: Fischer Daniel , Norel Raquel , Wolfson Haim , Nussinov Ruth
Published: May 2005

We describe the application of a method geared toward structural and surface comparison of proteins. The method is based on the Geometric Hashing Paradigm adapted from Computer Vision. It allows for comparison of any two sets of 3‐D coordinates, such as protein backbones, protein core or protein surface motifs, and small molecules such as drugs. Here we apply our method to 4 types of comparisons between pairs of molecules: (1) comparison of the backbones of two protein domains; (2) search for a predefined 3‐D Cαmotif within the full backbone of a domain; and in particular, (3) comparison of the surfaces of two receptor proteins; and (4) comparison of the surface of a receptor to the surface of a ligand. These aspects complement each other and can contribute toward a better understandingof protein structure and biomolecular recognition. Searches for 3‐D surface motifs can be carried out on either receptors or on ligands. The latter may result in the detection of pharmacophoric patterns. If the surfaces of the binding sites of either the receptors or of the ligands are relatively similar, surface superpositioning may aid significantly in the docking problem. Currently, only distance invariants are used in the matching, although additional geometric surface invariants are considered. The speed of our Geometric Hashing algorithm is encouraging, with a typical surface comparison taking only seconds or minutes of CPU time on a SUN 4 SPARC workstation. The direct application of this method to the docking problem is also discussed. We demonstrate the success of this methodin its application to two members of the globin family and to two dehydrogenases. © 1993 Wiley‐Liss, Inc.
Automated docking in crystallography: Analysis of the substrates of aconitase
Authors: Goodsell David S. , Lauble Hans , Stout C. David , Olson Arthur J.
Published: May 2005

Automated docking of substrates to proteins of known structure aids the process of crystallographic analysis in two ways. First, automated docking can be used to generate a small number of starting models for substrates using only protein coordinates from an early stage of refinement. Second, automated docking provides a method for exploring aspects of catalysis that are inaccessible to crystallography by postulating binding modes of catalytic intermediates. This paper describes the use of automated docking to explore the binding of substrates to aconitase. The technique starts with a substrate molecule in an arbitrary configuration and position and finds favorable docked configrations in a (static) protein active site based on a molecular mechanics type force field. Using protein coordinates from an early stage of refinement of an aconitase‐isocitrate complex, we successfully predicted the binding configuration of isocitrate. Four configurations were found, the energetically most favorable of which fit the observed electron density well and was used as a starting model for further refinement. Two configurations were found in citrate docking experiments, the second of which approximates the mode of substrate binding in an aconitasenitrocitrate complex. We were also able to propose two binding modes of the catalytic intermediate cis‐aconitate. These correspond closely to the isocitrate and the citrate binding modes. The relation of these new results to the proposed reaction mechanism is discussed. © 1993 Wiley‐Liss, Inc.
Performance evaluation of amino acid substitution matrices
Authors: Henikoff Steven , Henikoff Jorja G.
Published: May 2005

Several choices of amino acid substitution matrices are currently available for searching and alignment applications. These choices were evaluated using the BLAST searching program, which is extremely sensitive to differences among matrices, and the Prosite catalog, which lists members of hundreds of protein families. Matrices derived directly from either sequence‐based or structurebased alignments of distantly related proteins performed much better overall than extrapolated matrices based on the Dayhoff evolutionary model. Similar results were obtained with the FASTA searching program. Improved performance appears to be general rather than family‐specific, reflecting improved accuracy in scoring alignments. An implementation of a multiple matrix strategy was also tested. While no combination of three matrices performed as well as the single best matrix, BLOSUM 62, good results were obtained using a combination of sequence‐based and structure‐based matrices. This hybrid set of matrices is likely to be useful in certain situations. Our results illustrate the importance of matrix selection and value of a comprehensive approach to evaluation of protein comparison tools. © 1993 Wiley‐Liss, Inc.
Primary structure effects on peptide group hydrogen exchange
Authors: Bai Yawen , Milne John S. , Mayne Leland , Englander S. Walter
Published: May 2005

The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest‐neighbor blocking and inductive effects was tested in oligo‐and polypeptides and, suprisingly, confirmed. Reference rates for alanine‐containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo‐ and polypeptides. The application of this approach to protein studies is discussed. © 1993 Wiley‐Liss, Inc.
Isotope effects in peptide group hydrogen exchange
Authors: Connelly Gregory P. , Bai Yawen , Jeng Mei‐Fen , Englander S. Walter
Published: May 2005

Kinetic and equilibrium isotope effects in peptide group hydrogen exchange reactions were evaluated. Unlike many other reactions, Kinetic isotope effects in amide hydrogen exchange are small because exchange pathways are not limited by bondbreaking steps. Rate constants for the acid‐cat‐alyzed exchange of peptide group NH, ND, and NT in H2O are essentially identical, but a solvent esotope effect doubles the rate in D2O. Rate constants for base‐catalyzed exchange in H2O decrease slowly in the order NH > ND > NT. The alkaline rate constant in D2O is very close to that in H2O when account is taken of the glass electrode pH artifact and the difference in solvent ionization constant. Small equilibrium isotope effects lead to an excess equilibrium accumulation of the heavier isotopes by the peptide group. Results obtained are expressed in terms of rate constants for the random coil polypeptide, poly‐DL‐alanine, to provide reference rates for protein hydrogen exchange studies as described in Bai et al. [preceding paper in this issue]. © 1993 Wiley‐Liss, Inc.
Molecular basis of cooperativity in protein folding IV. Core: A general cooperative folding model
Authors: Freire Ernesto , Haynie Donald T. , Xie Dong
Published: May 2005

The cooperative nature of the protein folding process is independent of the characteristic fold and the specific secondary structure attributes of a globular protein. A general folding/unfolding model should, therefore, be based upon structural features that transcend the peculiarities of α‐helices, β‐sheets, and other structural motifs found in proteins. The studies presented in this paper suggest that a single structural characteristic common to all globular proteins is essential for cooperative folding. The formation of a partly folded state from the native state results in the exposure to solvent of two distinct regions: (1) the portions of the protein that are unfolded; and (2) the “complementary surfaces,” located in the regions of the protein that remain folded. The cooperative character of the folding/unfolding transition is determined largely by the energetics of exposing complementary surface regions to the solvent. By definition, complementary regions are present only in partly folded states; they are absent from the native and unfolded states. An unfavorable free energy lowers the probability of partly folded states and increases the cooperativity of the transition. In this paper we present a mathematical formulation of this behavior and develop a general cooperative folding/unfolding model, termed the “complementary region” (CORE) model. This model successfully reproduces the main properties of folding/unfolding transitions without limiting the number of partly folded states accessible to the protein, thereby permitting a systematic examination of the structural and solvent conditions under which intermediates become populated. It is shown that the CORE model predicts two‐state folding/unfolding behavior, even though the two‐state character is not assumed in the model. © 1993 Wiley‐Liss, Inc.
Solution structure of tertiapin determined using nuclear magnetic resonance and distance geometry
Authors: Xu Xiaobing , Nelson Jeffrey W.
Published: May 2005

The solution structure of tertiapin, a 21‐residue bee venom peptide, has been characterized by circular dichroism (CD), two‐dimensional nuclear magnetic resonance (NMR) spectroscopy, and distance geometry. A total of 21 lowest error structures were obtained from distance geometry calculations. Superimposition of these structures shows that the backbone of tertiapin is very well defined. One type‐I reverse turn from residue 4 to 7 and an α‐helix from residue 12 to 19 exist in the structure of tertiapin. The α‐helical region is best defined from both conformational analysis and structural superimposition. The overall three‐dimensional structure of tertiapin is highly compact resulting from side chain interactions. The structural information obtained from CD and NMR are compared for both tertiapin and apamin (ref. 3), another bee venom peptide. Tertiapin and apamin have some similar secondary structure, but display different tertiary structures. © 1993 Wiley‐Liss, Inc.
Orientational sampling and rigid‐body minimization in molecular docking
Authors: Meng Elaine C. , Gschwend Daniel A. , Blaney Jeffrey M. , Kuntz Irwin D.
Published: May 2005

The biological activities of proteins depends on specific molecular recognition and binding. Computational methods for predicting binding modes can facilitate the discovery and design of ligands and yeild information on the factors governing complementarity. The DOCK suite of programs has been applied to several systems; here, the degree of orientational sampling required to reproduce and identify known binding modes, with and without rigid‐body energy minimization, is investigated for four complexes. There is a tradeoff between sampling and minimization. The known binding modes can be identified with intensive sampling alone (10,000 to 20,000 orientations generated per system) or with moderate sampling combined with minimization. Optimization improves energies significantly, particularly when steric clashes are present, and brings many orientations closer to the experimentally observed position. Whether or not minimization is performed, however, sampling must be sufficient to find at least one structure in the vicinity of the presumed true binding mode. Hybrid approaches combining docking and minimization are promising and will become more viable with the use of faster algorithms and the judicious selection of fewer orientations for minimization. © 1993 Wiley‐Liss, Inc.
Crystallization and prelilminary X‐ray investigation of barster, the intracellular inhibitor of barnase
Authors: Guillet Valérie , Lapthorn Adrian , Fourniat Jacky , Benoit Jean‐Pierre , Hartley Robert W. , Mauguen Yves
Published: May 2005

Crystals of barstar, the intracellular inhibitor of the extracellular ribonuclease produced by Bacillus amyloliquefaciens (barnase), were obtained through vapor phase equilibration using the hanging drop technique. Three crystal forms have been characterized. Forms I and II, crystallized eithr in potetragonal; they exhibit a superstructure along the c‐axis. Form III crystals, suitable for a high resolution structure determination, were grown from 55‐65% ammomnium sulfate. This crystal form is hexagonal and diffracts to at least 2 Å resolution at a synchrotron radiation source. It belongs to the hexagonal space group P6, with unit cell dimensions a = b = 143.6 Å, c = 35.6 Å. There are four molecules of barstar in the asymmetric unit. X‐ray data have been collected to 2.2 Å Bragg sapcing. The structure determination is underway in order to analyze conformational changes of barstar upon complexation with barnas. © 1993 Wiley‐Liss, Inc.
Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 Å resolution: Proof for a single Mg2+‐binding site
Authors: Katayanagi Katsuo , Okumura Mika , Morikawa Kosuke
Published: May 2005

To obtain more precise insight into the Mg2+‐binding site essential for RNase HI catalytic activity, we have determined the crystal structure of E. coli RNase HI in complex with Mg2+. The analyzed cocrystal, which is not isomorphous with the Mg2+‐free crystal previously refined at 1.48 Å resolution, was grown at a high MgSO4 concentration more than 100 mM so that even weakly bound Mg2+ sites could be identified. The structure was solved by the molecular replacement method, using the Mg2+‐free crystal structure as a search model, and was refined to give a final R‐value of 0.190 for intensity data from 10 to 2.8 Å, using the XPLOR and PROLSQ programs. The backbone structures are in their entirety very similar to each other between the Mg2+‐bound and the metal‐free crystals, except for minor regions in the enzyme interface with the DNA/RNA hybrid. The active center clearly revealed a single Mg2+ atom located at a position almost identical to that previously found by the soaking method. Although the two metal‐ion mechanism had been suggested by another group (Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y. Science 249:1398‐1405, 1990) and partially supported by the crystallographic study of inactive HIV‐1 RT RNase H fragment (Davies, J.F., II, Hostomska, Z., Hostomsky, Z., Jordan, S.R., Matthews, D. Science 252:88‐95, 1991), the present result excludes the possibility that RNase HI requires two metal‐binding sites for activity. In contrast to the features in the metal‐free enzyme, the side chains of Asn‐44 and Glu‐48 are found to form coordinate bonds with Mg2+ in the metal‐bound crystal. © 1993 Wiley‐Liss, Inc.
Hundreds of ankyrin‐like repeats in functionally diverse proteins: Mobile modules that cross phyla horizontally?
Authors: Bork Peer
Published: May 2005

Based on pattern searches and systematic database screening, almost 650 different ankyrin‐like (ANK) repeats from nearly all phyla have been identified; more than 150 of them are reported here for the first time. Their presence in functionally diverse proteins such as enzymes, toxins, and transcription factors strongly suggests domain shuffling, but their occurrence in prokaryotes and yeast excludes exon shuffling. The spreading mechanism remains unknown, but in at least three cases horizontal gene transfer appears to be involved. ANK repeats occur in at least four consecutive copies. The terminal repeats are more variable in sequence. One feature of the internal repeats is a predicted central hydrophobic α‐helix, which is likely to interact with other repeats. The functions of the ankyrin‐like repeats are compatible with a role in protein‐protein interactions. © 1993 Wiley‐Liss, Inc.
A method to recognize distant repeats in protein sequences
Authors: Heringa Jaap , Argos Patrick
Published: May 2005

An automated algorithm is presented that delineates protein sequence fragments which display similarity. The method incorporates a selection of a number of local nonoverlapping sequence alignments with the highest similarity scores and a graphtheoretical approach to elucidate the consistent start and end points of the fragments comprising one or more ensembles of related subsequences. The procedure allows the simultaneous identification of different types of repeats within one sequence. A multiple alignment of the resulting fragments is performed and a consensus sequence derived from the ensemble(s). Finally, a profile is constructed form the multiple alignment to detect possible and more distant members within the sequence. The method tolerates mutations in the repeats as well as insertions and deletions. The sequence spans between the various repeats or repeat clusters may be of different lengths. The technique has been applied to a number of proteins where the repeating fragments have been derived from information additional to the protein sequences. © 1993 Wiley‐Liss, Inc.
Essential dynamics of proteins
Authors: Amadei Andrea , Linssen Antonius B. M. , Berendsen Herman J. C.
Published: May 2005

Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an “essential” subspace containing only a few degrees of freedom in which anharmonic motion occurs that comprises most of the positional fluctuations; and (2) the remaining space in which the motion has a narrow Gaussian distribution and which can be considered as “physically constrained.” If overall translation and rotation are eliminated, the two spaces can be constructed by a simple linear transformation in Cartesian coordinate space, which remains valid over several hundred picoseconds. The transformation follows from the covariance matrix of the positional deviations. The essential degrees of freedom seem to describe motions which are relevant for the function of the protein, while the physically constrained subspace merely describes irrelevant local fluctuations. The near‐constraint behavior of the latter subspace allows the separation of equations of motion and promises the possibility of investigating independently the essential space and performing dynamic simulations only in this reduced space. © 1993 Wiley‐Liss, Inc.
Alpha helix capping in synthetic model peptides by reciprocal side chain–main chain interactions: Evidence for an N terminal “capping box”
Authors: Zhou Hongxing X. , Lyu Pingchiang , Wemmer David E. , Kallenbach Neville R.
Published: May 2005

A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H‐bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H‐bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser‐Glu‐Asp‐Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain–main chain interactions in a varient sequence using 1H NMR, and find that the postulated reciprocal side chain‐backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser‐Glu‐Asp‐Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two‐dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser‐Glu‐Asp‐Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain–main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.
The Structure of Trypanosoma cruzitrypanothione Reductase in the Oxidized and NADPH Reduced State
Authors: Lantwin Christina B. , Schlichting Ilme , Kabsch Wolfgang , Pai Emil F. , Krauth‐Siegel R. Luise
Published: May 2005

The three‐dimensional structure of trypanothione reductase (TR) (EC 1.6.4.8) from Trypanosoma cruzi has been solved at 0.33 nm resolution by molecular replacement using the structure of C. fasciculata TR as a starting model. Elucidation of the T. cruzi TR structure represents the first step in the rational design of a drug against Chagas' disease. The structure of T. cruzi TR is compared with those of C. fasciculata TR as well as human and E. coli glutathione reductase (GR). In the FAD‐binding domain, TR has two insertions, each about 10 residues long, which do not occur in GR. The first one is a rigid loop stabilizing the position of helix 91–117 which is responsible for the wider active site of TR as compared to GR. The second insertion does not occur where it is predicted by sequence alignment; rather the residues extend three strands of the 4‐stranded β‐sheet by one or two residues each. This increases the number of hydrogen bonds within the sheet structure. The structure of the NADPH.TR complex has been solved at 0.33 nm resolution. The nicotinamide ring is sandwiched between the flavin ring and the side chain of Phe‐198 which undergoes the same conformational change upon coenzyme binding as Tyr‐197 in GR. In addition to Arg‐222 and Arg‐228, which are conserved in TR and GR, Tyr‐221—the last residue of the second β‐sheet strand of the βαβ dinucleotide binding fold—is in hydrogen bonding distance to the 2′ phosphate group of NADPH. © 1994 John Wiley & Sons, Inc.
Correlated mutations and residue contacts in proteins
Authors: Göbel Ulrike , Sander Chris , Schneider Reinhard , Valencia Alfonso
Published: May 2005

The maintenance of protein function and structure constrains the evolution of amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication of probable physical contact in three dimensions. Here we present a simple and general method to analyze correlations in mutational behavior between different positions in a multiple sequence alignment. We then use these correlations to predict contact maps for each of 11 protein families and compare the result with the contacts determined by crystallography. For the most strongly correlated residue pairs predicted to be in contact, the prediction accuracy ranges from 37 to 68% and the improvement ratio relative to a random prediction from 1.4 to 5.1. Predicted contact maps can be used as input for the calculation of protein tertiary structure, either from sequence information alone or in combination with experimental information. © 1994 John Wiley & Sons, Inc.
Monte carlo simulations of protein folding. I. Lattice model and interaction scheme
Authors: Kolinski Andrzej , Skolnick Jeffrey
Published: May 2005

A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three‐dimensional structure is proposed. The reduced representation of the protein α‐carbon backbone employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers. In particular, coarser and finer lattice backbone descriptions are used. The coarser (finer) lattice represents Cα traces of native proteins with an accuracy of 1.0 (0.7) Å rms. Folding is simulated by means of very fast Monte Carlo lattice dynamics. The potential of mean force, predominantly of statistical origin, contains several novel terms that facilitate the cooperative assembly of secondary structure elements and the cooperative packing of the side chains. Particular contributions to the interaction scheme are discussed in detail. In the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353–366, 1994), the method is applied to three small globular proteins. © 1994 John Wiley & Sons, Inc.