Crystalography

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1.     
   Ogata K. and Wodak S.J.
   Conserved water molecules in MHC class-I proteins and their putative structural and functions roles.
   Protein Engineering 15: 697-705

A set of conserved water positions making direct contacts with the alpha1 and alpha2 domains of the MHC class-I protein was identified by a cluster analysis in 12 high-resolution crystal structures of proteins from different allele types and different species, comprising human, mouse and rat. The analysis revealed a total of 63 clusters, corresponding to water molecules, whose positions are conserved in half or more of the analyzed structures. Analysis of these clusters shows that the most conserved water positions-those appearing in the largest fraction of the structures-were also the most accurately defined, as measured by their normalized crystallographic B-factor. Not too surprisingly, these positions displayed better overlap and formed more H-bonds with the protein. In a second part of this work, a detailed analysis is presented of three of the most conserved water positions and their putative structural and functional roles are discussed. The most highly conserved of the three appears to play an important role in stabilizing the conformation of a twisted beta-turn between residues 118 and 122 (numbering of HLA-B3501, PDB code 1A1N). An equivalent water molecule was found to be associated with a similar beta-turn in 43 unrelated structures surveyed in the PDB, leading to the suggestion that this water molecule plays an important structural role in this type of turn. The second water molecule makes hydrogen bonds with residues lining pocket B in the peptide-binding groove and is suggested to play a role in modulating peptide recognition. The third highly conserved water molecule is located at the first kink of the alpha2 helix, possibly playing a role in determining the position of the N-terminal segment of that helix, which also carries side chains in contact with the bound peptide. This information on conserved water positions in MHC class-I molecules should be helpful in modeling interactions with bound peptide antigens and in designing new peptides with tailor-made affinities.



2.     
   Wodak S.J. & Janin J.
   The structural basis of macromolecular recognition.
   Advances in Protein Chemistry 61: 9-73.


3.     
   Das U Chen S Fuxreiter M Vaguine AA Richelle J Berman HM Wodak SJ.
   Checking nucleic acid crystal structures.
   Acta Crystallogr D Biol Crystallogr.57: 813-28.

The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of the backbone. One of the local indicators, the density index, is particularly useful in spotting regions of the model that fit poorly in the electron density. Using this parameter, the quality of crystallographic water positions in the analyzed structures was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. The possibility that cases of poorly positioned water molecules are symptomatic of more widespread problems with the structure as a whole is also raised.



4. Wodak S.J. Vaguine A.A. Richelle J. Das U.& Pontius J.
   Assessing the quality of MacromolecularStructures
   International Tables Volume F Chapter 21
5.     
   Vaguine A.V. Richelle J. & Wodak S.J.
   SFCHECK: a unified set of procedures forevaluating the quality of macromolecular structure-factor data andtheir agreement with the atomic model.
   Acta Cryst. D55 191-205

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.



6.     
   Alberts I. Nadassy K. and Wodak S.J.
   Analysis of zinc binding sites in proteincrystal structures
   Protein Science 7(8) 1700-1716

The geometrical properties of zinc binding sites in a data set of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our data set and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.



7. EU BIOTECHNOLOGY 3D Validation projectnetwork (Wilson K.S. Butterworth S. Dauter Z. Lamzin V.S. WodakS.J. Pontius J. Richelle J. Vaguine A. Sander C. Hooft R.W.W. Vriend G. Thornton J.M. Laskowski R.A. MacArthur M.W. Dodson E.J. Murshudov G. Oldfield T.J. Kaptein R. Rullmann J.A.C.
   (1997). Who checks the checkers? Fourvalidation tools applied to eight atomic resolution structures.
   J. Mol. Biol. 276 417-436
8. Wodak S.J. Pontius J. Vaguine A. andRichelle J.
   Procedures for assessing the quality of X-raystructures of macromolecules
   In Proceedings of the 1996 meeting of theIUCr Macromolecular Computing School.
9.     
   Pontius J. Richelle J. and Wodak S.J.
   Deviations from standard atomic volumes as aquality measure for protein crystal structures.
   J. Mol. Biol. 264(1) 121-136

Standard ranges of atomic and residue volumes are computed in 64 highly resolved and well-refined protein crystal structures using the classical Voronoi procedure. Deviations of the atomic volumes from the standard values, evaluated as the volume Z-scores, are used to assess the quality of protein crystal structures. To score a structure globally, we compute the volume Z-score root mean square deviation (Z-score rms), which measures the average magnitude of the volume irregularities in the structure. We find that the Z-score rms decreases as the resolution and R-factor improve, consistent with the fact that these improvements generally reflect more accurate models. From the Z-score rms distribution in structures with a given resolution or R-factor, we determine the normal limits in Z-score rms values for structures solved at that resolution or R-factor. Structures whose Z-score rms exceeds these limits are considered as outliers. Such structures also exhibit unusual stereochemistry, as revealed by other analyses. Absolute Z-scores of individual atoms are used to identify problems in specific regions within a protein model. These Z-scores correlate fairly well with the atomic B-factors, and atoms having absolute Z-scores > 3, occur at or near regions in the model where programs such as PROCHECK identify unusual stereochemistry. Atomic volumes, themselves not directly restrained in crystallographic refinement, can thus provide an independent, rather sensitive, measure of the quality of a protein structure. The volume-based structure validation procedures are implemented in the program PROVE (PROtein Volume Evaluation), which is accessible through the World Wide Web.



10.     
    EU BRIDGE Database project consortium: GrayP.M.D. Kemp G.J.L. Rawlings C.J. Brown N.P. Sander C. ThorntonJ.M. Orengo C.M. Wodak S.J. & Richelle J.
    Molecular structure information and databases.
    TIBS 21(7) 251-256

The current status and future outlook of macromolecular structure databases and information handling, with particular reference to European databases, are reviewed. Issues concerning the efficiency with which data are represented, validated, archived and accessed are discussed in view of the fast growing body of information on structures of biological macromolecules.



11.     
    Wodak S.J.
    Extending molecular systematics to the third dimension.
    Nature Structural Biology 3(7) 575-578.


12. Wodak S.J. Pontius J.U. Vaguine A. andRichelle J.
    Validating protein structures: fromconsistency checking to quality assessment
    In W.N. Hunter J.M. Thornton and S. Bailey(eds.) Making the Most of your Model. Proceedings of the CCP4 studyweekend held at Chester United Kingdom 1995 41-51.
13.     
    Gutschina A. Sansom Cl. Prvost M. RichelleJ. Wodak S.J. Wlodawer Al. and Weber I.T.
    Energy calculations and analysis of HIV-1protease-inhibitor crystal structures.
    Protein Eng. 7(3) 309-317

The interactions between HIV-1 protease and its bound inhibitors have been investigated by molecular mechanics calculations and by analysis of crystal structures of the complexes in order to determine general rules for inhibitor and substrate binding to the protease. Fifteen crystal structures of HIV-1 protease with different peptidomimetic inhibitors showed conservation of hydrogen bond interactions between the main chain C = O and NH groups of the inhibitors and the C = O and NH groups of the protease extending from P3 C = O to P3' NH. The mean length of the hydrogen bonds between the inhibitor and the flexible flaps and the conserved water molecule (2.9 A) is slightly shorter than the mean length of hydrogen bonds between the inhibitor and the more rigid active site region (3.1 A) of the protease. The two hydrogen bonds between the conserved water and P2 and P1' carbonyl oxygen atoms of the inhibitor are the shortest and are predicted to be important for the tight binding of inhibitors. Molecular mechanics analysis of three crystal structures of HIV-1 protease with different inhibitors with independent calculations using the programs Discover and Brugel gave an estimate of 56-68% for the contribution of all the inhibitor main chain atoms to the total calculated protease-inhibitor interaction energy. The contribution of individual inhibitor residues to the interaction energy was calculated using Brugel. The main chain atoms of residue P2 had a consistently large favorable contribution to the total interaction energy, probably due to the presence of the two short hydrogen bonds to the flexible flap.(ABSTRACT TRUNCATED AT 250 WORDS)



14.     
    Janin J. and Wodak S.J.
    The quaternary structure of Carbonmonoxy Hemoglobin Ypsilanti.
    Proteins 15 1-4

We present a geometric analysis of the allosteric interface in the new Y state quaternary structure observed in liganded mutant hemoglobin Ypsilanti (beta 99 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 alpha beta dimers about an axis which is approximately parallel to the dimer axis of pseudosymmetry, 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.



15.     
    Jenkins J. Janin J. Rey F. Chiadmi M. van Tilbeurgh H. Lasters I. De Maeyer M. Van Belle D. Wodak S.J. Lauwereys M. Stanssens P. Mrabet N.T. Snauwaert J. Matthyssens G.and Lambeir A.-M.
    Protein engineering of xylose (glucose)isomerase from Actinoplanes missouriensis 1. Crystallography and site-directed analysis of metal binding sites.
    Biochemistry 31(24) 5449-5458

The structure and function of the xylose (glucose) isomerase from Actinoplanes missouriensis have been analyzed by X-ray crystallography and site-directed mutagenesis after cloning and overexpression in Escherichia coli. The crystal structure of wild-type enzyme has been refined to an R factor of 15.2% against diffraction data to 2.2-A resolution. The structures of a number of binary and ternary complexes involving wild-type and mutant enzymes, the divalent cations Mg2+, Co2+, or Mn2+, and either the substrate xylose or substrate analogs have also been determined and refined to comparable R factors. Two metal sites are identified. Metal site 1 is four-coordinated and tetrahedral in the absence of substrate and is six-coordinated and octahedral in its presence; the O2 and O4 atoms of linear inhibitors and substrate bind to metal 1. Metal site 2 is octahedral in all cases; its position changes by 0.7 A when it binds O1 of the substrate and by more than 1 A when it also binds O2; these bonds replace bonds to carboxylate ligands from the protein. Side chains involved in metal binding have been substituted by site-directed mutagenesis. The biochemical properties of the mutant enzymes are presented. Together with structural data, they demonstrate that the two metal ions play an essential part in binding substrates, in stabilizing their open form, and in catalyzing hydride transfer between the C1 and C2 positions.



16.     
    Rey F. Jenkins J. Janin J. Lasters I. Alard P. Claessens M. Matthyssens G. and Wodak S.J.
    Structural analysis of the 2.8 model of xyloseisomerase from Actinoplanes missouriensis.
    Proteins 4 165-172.

The structure of Xylose isomerase (X.I.) from Actinoplanes missouriensis has been solved to 2.8 Angstroms resolution. Phases were determined from a single Eu3+ derivative and from the noncrystallographic 222 symmetry of the tetrameric molecule. An atomic model was built and subjected to restrained crystallographic refinement. The resulting model is shown to be closely similar to the recently reported X.I.'s structures from three other bacterial sources. Each monomer is found to be composed of an eight-stranded alpha/beta "T.I.M." barrel forming an N-terminal domain of 328 residues followed by a large loop of 66 residues embracing an adjacent subunit. Analysis of intersubunit packing shows that the X.I. tetramer is an assembly of two tight dimers. The beta barrel fits a simple hyperboloid model as other T.I.M. barrels do. The active site, identified as the binding site for the inhibitor xylitol, is located at the carboxyl end of the beta strands in the barrel next to a pair of binding sites for Eu3+ ions, which are assumed to be sites for the divalent ions involved in catalysis. Active sites in the tetramer are oriented towards the interface between dimers. It is suggested that subunit interfaces might stabilize the active site region and this might explain the oligomeric nature of other alpha/beta barrel enzymes.



17. Renneboog C. Delhaise Ph. and Wodak S.J.
    The influence of crystal packing on the 3-Dconformation of insulin.
    Archives Internationales de Physiologie etde Biochimie 89 B192.
18. Wyckoff H.W. Carlson W. and Wodak S.J.
    The structure of nucleic-acid protein complexes as evidenced by dinucleoside complexes with RNase-S. InNucleic acid-protein recognition.
    New York Academic Press. 569-580.
19.     
    Wodak S.J. Liu M.Y. and Wyckoff H.W.
    The structure of cytidilyl-(2' 5')-adenosine when bound to pancreatic ribonuclease. S J.Mol.Biol. 116 855-875.


20. Wodak S.J.
    The crystal structure of Heliotrine apyrrolizidine alkaloid monester Acta Cryst. 31 569-573.
21. Sussman J.L. and Wodak S.J.
    The crystal structure of Fulvine apyrrolizidine alkaloid Acta Cryst. 29 2918-2926.