Nucleic Acids Research Advance Access published online on April 22, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm216
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Web Server Paper |
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
1Department of Biochemistry, Duke University, Durham, NC, USA and 2Department of Computer Science, UNC Chapel Hill, Chapel Hill, NC, USA
*To whom correspondence should be addressed. Tel: +1-919-684-6010; Email: dcr{at}kinemage.biochem.duke.edu
Received January 26, 2007. Revised March 20, 2007. Accepted March 28, 2007.
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. R. Clark, G. M. Sawyer, S. P. Robertson, and A. J. Sutherland-Smith Skeletal dysplasias due to filamin A mutations result from a gain-of-function mechanism distinct from allelic neurological disorders Hum. Mol. Genet., December 15, 2009; 18(24): 4791 - 4800. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Bellinzoni, S. Buroni, F. Schaeffer, G. Riccardi, E. De Rossi, and P. M. Alzari Structural Plasticity and Distinct Drug-Binding Modes of LfrR, a Mycobacterial Efflux Pump Regulator J. Bacteriol., December 15, 2009; 191(24): 7531 - 7537. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Diacovich, A. Dumont, D. Lafitte, E. Soprano, A.-A. Guilhon, C. Bignon, J.-P. Gorvel, Y. Bourne, and S. Meresse Interaction between the SifA Virulence Factor and Its Host Target SKIP Is Essential for Salmonella Pathogenesis J. Biol. Chem., November 27, 2009; 284(48): 33151 - 33160. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. I. Biterova and J. J. Barycki Mechanistic Details of Glutathione Biosynthesis Revealed by Crystal Structures of Saccharomyces cerevisiae Glutamate Cysteine Ligase J. Biol. Chem., November 20, 2009; 284(47): 32700 - 32708. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. de Alba Structure and Interdomain Dynamics of Apoptosis-associated Speck-like Protein Containing a CARD (ASC) J. Biol. Chem., November 20, 2009; 284(47): 32932 - 32941. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. MacKenzie, L. E. Tailford, A. M. Hemmings, and N. Juge Crystal Structure of a Mucus-binding Protein Repeat Reveals an Unexpected Functional Immunoglobulin Binding Activity J. Biol. Chem., November 20, 2009; 284(47): 32444 - 32453. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. S. Berkholz, P. B. Krenesky, J. R. Davidson, and P. A. Karplus Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry Nucleic Acids Res., November 11, 2009; (2009) gkp1013v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Schreier, C. Stumpp, S. Wiesner, and B. Hocker Computational design of ligand binding is not a solved problem PNAS, November 3, 2009; 106(44): 18491 - 18496. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Koutmos, S. Datta, K. A. Pattridge, J. L. Smith, and R. G. Matthews Insights into the reactivation of cobalamin-dependent methionine synthase PNAS, November 3, 2009; 106(44): 18527 - 18532. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Zhang, J.-h. Liu, W. Yang, T. Springer, M. Shimaoka, and J.-h. Wang Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1 PNAS, October 27, 2009; 106(43): 18345 - 18350. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Berrisford and L. A. Sazanov Structural Basis for the Mechanism of Respiratory Complex I J. Biol. Chem., October 23, 2009; 284(43): 29773 - 29783. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Ruprecht, V. Yankovskaya, E. Maklashina, S. Iwata, and G. Cecchini Structure of Escherichia coli Succinate:Quinone Oxidoreductase with an Occupied and Empty Quinone-binding Site J. Biol. Chem., October 23, 2009; 284(43): 29836 - 29846. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Wei, Y. Yan, R. W. Carrell, and A. Zhou Crystal structure of protein Z-dependent inhibitor complex shows how protein Z functions as a cofactor in the membrane inhibition of factor X Blood, October 22, 2009; 114(17): 3662 - 3667. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Wojciak, N. Zhu, K. T. Schuerenberg, K. Moreno, W. S. Shestowsky, M. Hiraiwa, R. Sabbadini, and T. Huxford The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen PNAS, October 20, 2009; 106(42): 17717 - 17722. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Liu, A. H. R. Shim, and X. He Structural Characterization of the Ectodomain of a Disintegrin and Metalloproteinase-22 (ADAM22), a Neural Adhesion Receptor Instead of Metalloproteinase: INSIGHTS ON ADAM FUNCTION J. Biol. Chem., October 16, 2009; 284(42): 29077 - 29086. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Vila, Y. A. Arnautova, O. A. Martin, and H. A. Scheraga Quantum-mechanics-derived 13C{alpha} chemical shift server (CheShift) for protein structure validation PNAS, October 6, 2009; 106(40): 16972 - 16977. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Li, Y. Wang, H. Jiang, and J. Deng Crystal structure of Manduca sexta prophenoloxidase provides insights into the mechanism of type 3 copper enzymes PNAS, October 6, 2009; 106(40): 17002 - 17006. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Kobayashi, H. Utsunomiya, H. Yamanaka, Y. Sei, N. Katunuma, K. Okamoto, and H. Tsuge Structural Basis for the Kexin-like Serine Protease from Aeromonas sobria as Sepsis-causing Factor J. Biol. Chem., October 2, 2009; 284(40): 27655 - 27663. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. T. Larson, F. Parussini, M.-H. Huynh, J. D. Giebel, A. M. Kelley, L. Zhang, M. Bogyo, E. A. Merritt, and V. B. Carruthers Toxoplasma gondii Cathepsin L Is the Primary Target of the Invasion-inhibitory Compound Morpholinurea-leucyl-homophenyl-vinyl Sulfone Phenyl J. Biol. Chem., September 25, 2009; 284(39): 26839 - 26850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Zhao, G. Li, H. Schindelin, and W. J. Lennarz An Armadillo motif in Ufd3 interacts with Cdc48 and is involved in ubiquitin homeostasis and protein degradation PNAS, September 22, 2009; 106(38): 16197 - 16202. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. D. Kerr, J. H. Lee, C. J. Farady, R. Marion, M. Rickert, M. Sajid, K. C. Pandey, C. R. Caffrey, J. Legac, E. Hansell, et al. Vinyl Sulfones as Antiparasitic Agents and a Structural Basis for Drug Design J. Biol. Chem., September 18, 2009; 284(38): 25697 - 25703. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Linke, T. T. Caradoc-Davies, P. G. Young, T. Proft, and E. N. Baker The Laminin-Binding Protein Lbp from Streptococcus pyogenes Is a Zinc Receptor J. Bacteriol., September 15, 2009; 191(18): 5814 - 5823. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Korkut and W. A. Hendrickson Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase PNAS, September 15, 2009; 106(37): 15673 - 15678. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. K. Koski, R. Hieta, M. Hirsila, A. Ronka, J. Myllyharju, and R. K. Wierenga The Crystal Structure of an Algal Prolyl 4-Hydroxylase Complexed with a Proline-rich Peptide Reveals a Novel Buried Tripeptide Binding Motif J. Biol. Chem., September 11, 2009; 284(37): 25290 - 25301. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Xu, B. A. Traag, J. Willemse, D. McMullan, M. D. Miller, M.-A. Elsliger, P. Abdubek, T. Astakhova, H. L. Axelrod, C. Bakolitsa, et al. Structural and Functional Characterizations of SsgB, a Conserved Activator of Developmental Cell Division in Morphologically Complex Actinomycetes J. Biol. Chem., September 11, 2009; 284(37): 25268 - 25279. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. J. Lee, B. Rakic, M. Gilbert, W. W. Wakarchuk, S. G. Withers, and N. C. J. Strynadka Structural and Kinetic Characterizations of the Polysialic Acid O-Acetyltransferase OatWY from Neisseria meningitidis J. Biol. Chem., September 4, 2009; 284(36): 24501 - 24511. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. T. Gregory, H. Demirci, R. Belardinelli, T. Monshupanee, C. Gualerzi, A. E. Dahlberg, and G. Jogl Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG RNA, September 1, 2009; 15(9): 1693 - 1704. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. J. Nicolson, E. A. Bellomo, N. Wijesekara, M. K. Loder, J. M. Baldwin, A. V. Gyulkhandanyan, V. Koshkin, A. I. Tarasov, R. Carzaniga, K. Kronenberger, et al. Insulin Storage and Glucose Homeostasis in Mice Null for the Granule Zinc Transporter ZnT8 and Studies of the Type 2 Diabetes-Associated Variants Diabetes, September 1, 2009; 58(9): 2070 - 2083. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. A. Bowden, M. Crispin, S. C. Graham, D. J. Harvey, J. M. Grimes, E. Y. Jones, and D. I. Stuart Unusual Molecular Architecture of the Machupo Virus Attachment Glycoprotein J. Virol., August 15, 2009; 83(16): 8259 - 8265. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. McMahon, G. A. Roberts, K. A. Johnson, L. P. Cooper, H. Liu, J. H. White, L. G. Carter, B. Sanghvi, M. Oke, M. D. Walkinshaw, et al. Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance Nucleic Acids Res., August 1, 2009; 37(15): 4887 - 4897. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Zhang, N. S. Astrof, J.-H. Liu, J.-h. Wang, and M. Shimaoka Crystal structure of isoflurane bound to integrin LFA-1 supports a unified mechanism of volatile anesthetic action in the immune and central nervous systems FASEB J, August 1, 2009; 23(8): 2735 - 2740. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. H. Khoo, A. C. Joerger, S. M.V. Freund, and A. R. Fersht Stabilising the DNA-binding domain of p53 by rational design of its hydrophobic core Protein Eng. Des. Sel., July 1, 2009; 22(7): 421 - 430. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Champion, L. Kundrat, L. Regan, and S. J. Baserga A structural model for the HAT domain of Utp6 incorporating bioinformatics and genetics Protein Eng. Des. Sel., July 1, 2009; 22(7): 431 - 439. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Tralau, P. Lafite, C. Levy, J. P. Combe, N. S. Scrutton, and D. Leys An Internal Reaction Chamber in Dimethylglycine Oxidase Provides Efficient Protection from Exposure to Toxic Formaldehyde J. Biol. Chem., June 26, 2009; 284(26): 17826 - 17834. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Formentini, A. Macchiarulo, G. Cipriani, E. Camaioni, E. Rapizzi, R. Pellicciari, F. Moroni, and A. Chiarugi Poly(ADP-ribose) Catabolism Triggers AMP-dependent Mitochondrial Energy Failure J. Biol. Chem., June 26, 2009; 284(26): 17668 - 17676. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Xu, L. Yi, Y. Feng, L. Chen, and J. Liu Structural Insight into the Activation Mechanism of Human Pancreatic Prophospholipase A2 J. Biol. Chem., June 12, 2009; 284(24): 16659 - 16666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Zhang, Y.-F. Zhou, C.-Z. Zhang, X. Zhang, C. Lu, and T. A. Springer Structural specializations of A2, a force-sensing domain in the ultralarge vascular protein von Willebrand factor PNAS, June 9, 2009; 106(23): 9226 - 9231. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. J. Gourlay, I. Santi, A. Pezzicoli, G. Grandi, M. Soriani, and M. Bolognesi Group B Streptococcus Pullulanase Crystal Structures in the Context of a Novel Strategy for Vaccine Development J. Bacteriol., June 1, 2009; 191(11): 3544 - 3552. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kamenecka, J. Habel, D. Duckett, W. Chen, Y. Y. Ling, B. Frackowiak, R. Jiang, Y. Shin, X. Song, and P. LoGrasso Structure-Activity Relationships and X-ray Structures Describing the Selectivity of Aminopyrazole Inhibitors for c-Jun N-terminal Kinase 3 (JNK3) over p38 J. Biol. Chem., May 8, 2009; 284(19): 12853 - 12861. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Sato, C. Li, I. Salard, A. J. Thompson, M. J. Banfield, and C. Dennison Metal-binding loop length and not sequence dictates structure PNAS, April 7, 2009; 106(14): 5616 - 5621. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. E. Loughlin, R. E. Mansfield, P. M. Vaz, A. P. McGrath, S. Setiyaputra, R. Gamsjaeger, E. S. Chen, B. J. Morris, J. M. Guss, and J. P. Mackay The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences PNAS, April 7, 2009; 106(14): 5581 - 5586. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Ditzler, J. Sponer, and N. G. Walter Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme RNA, April 1, 2009; 15(4): 560 - 575. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. J. Miknis, E. F. Donaldson, T. C. Umland, R. A. Rimmer, R. S. Baric, and L. W. Schultz Severe Acute Respiratory Syndrome Coronavirus nsp9 Dimerization Is Essential for Efficient Viral Growth J. Virol., April 1, 2009; 83(7): 3007 - 3018. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. de Silva, F. W. Perrino, and T. Hollis DNA binding induces active site conformational change in the human TREX2 3'-exonuclease Nucleic Acids Res., April 1, 2009; 37(7): 2411 - 2417. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. J. Ruiz-Duenas, R. Pogni, M. Morales, S. Giansanti, M. J. Mate, A. Romero, M. J. Martinez, R. Basosi, and A. T. Martinez Protein Radicals in Fungal Versatile Peroxidase: CATALYTIC TRYPTOPHAN RADICAL IN BOTH COMPOUND I AND COMPOUND II AND STUDIES ON W164Y, W164H, AND W164S VARIANTS J. Biol. Chem., March 20, 2009; 284(12): 7986 - 7994. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Davis, K. Abdi, M. Machius, C. Brautigam, D. R. Tomchick, V. Bennett, and P. Michaely Localization and Structure of the Ankyrin-binding Site on {beta}2-Spectrin J. Biol. Chem., March 13, 2009; 284(11): 6982 - 6987. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Blackinton, M. Lakshminarasimhan, K. J. Thomas, R. Ahmad, E. Greggio, A. S. Raza, M. R. Cookson, and M. A. Wilson Formation of a Stabilized Cysteine Sulfinic Acid Is Critical for the Mitochondrial Function of the Parkinsonism Protein DJ-1 J. Biol. Chem., March 6, 2009; 284(10): 6476 - 6485. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Guardado-Calvo, G. C. Fox, A. L. Llamas-Saiz, and M. J. van Raaij Crystallographic structure of the {alpha}-helical triple coiled-coil domain of avian reovirus S1133 fibre J. Gen. Virol., March 1, 2009; 90(3): 672 - 677. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. McGowan, C. J. Porter, J. Lowther, C. M. Stack, S. J. Golding, T. S. Skinner-Adams, K. R. Trenholme, F. Teuscher, S. M. Donnelly, J. Grembecka, et al. From the Cover: Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase PNAS, February 24, 2009; 106(8): 2537 - 2542. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Russo, J.-E. Schweitzer, T. Polen, M. Bott, and E. Pohl Crystal Structure of the Caseinolytic Protease Gene Regulator, a Transcriptional Activator in Actinomycetes J. Biol. Chem., February 20, 2009; 284(8): 5208 - 5216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Watanabe, J. G. Heddle, K. Kikuchi, S. Unzai, S. Akashi, S.-Y. Park, and J. R. H. Tame The nature of the TRAP-Anti-TRAP complex PNAS, February 17, 2009; 106(7): 2176 - 2181. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Guhaniyogi, I. Sohar, K. Das, A. M. Stock, and P. Lobel Crystal Structure and Autoactivation Pathway of the Precursor Form of Human Tripeptidyl-peptidase 1, the Enzyme Deficient in Late Infantile Ceroid Lipofuscinosis J. Biol. Chem., February 6, 2009; 284(6): 3985 - 3997. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Krieg, F. Huche, K. Diederichs, N. Izadi-Pruneyre, A. Lecroisey, C. Wandersman, P. Delepelaire, and W. Welte Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex PNAS, January 27, 2009; 106(4): 1045 - 1050. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. J. Baker, K. L. Britton, M. Fisher, J. Esclapez, C. Pire, M. J. Bonete, J. Ferrer, and D. W. Rice Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily PNAS, January 20, 2009; 106(3): 779 - 784. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Lafrance-Vanasse, M. Lefebvre, P. Di Lello, J. Sygusch, and J. G. Omichinski Crystal Structures of the Organomercurial Lyase MerB in Its Free and Mercury-bound Forms: INSIGHTS INTO THE MECHANISM OF METHYLMERCURY DEGRADATION J. Biol. Chem., January 9, 2009; 284(2): 938 - 944. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Emami, E. Topakas, T. Nagy, J. Henshaw, K. A. Jackson, K. E. Nelson, E. F. Mongodin, J. W. Murray, R. J. Lewis, and H. J. Gilbert Regulation of the Xylan-degrading Apparatus of Cellvibrio japonicus by a Novel Two-component System J. Biol. Chem., January 9, 2009; 284(2): 1086 - 1096. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. A. Springer Structural basis for selectin mechanochemistry PNAS, January 6, 2009; 106(1): 91 - 96. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Oswald, S. H. J. Smits, M. Hoing, L. Sohn-Bosser, L. Dupont, D. Le Rudulier, L. Schmitt, and E. Bremer Crystal Structures of the Choline/Acetylcholine Substrate-binding Protein ChoX from Sinorhizobium meliloti in the Liganded and Unliganded-Closed States J. Biol. Chem., November 21, 2008; 283(47): 32848 - 32859. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Guardado-Calvo, L. Vazquez-Iglesias, J. Martinez-Costas, A. L. Llamas-Saiz, G. Schoehn, G. C. Fox, X. L. Hermo-Parrado, J. Benavente, and M. J. van Raaij Crystal Structure of the Avian Reovirus Inner Capsid Protein {sigma}A J. Virol., November 15, 2008; 82(22): 11208 - 11216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. E. C. Caines, H. Zhu, M. Vuckovic, L. M. Willis, S. G. Withers, W. W. Wakarchuk, and N. C. J. Strynadka The Structural Basis for T-antigen Hydrolysis by Streptococcus pneumoniae: A TARGET FOR STRUCTURE-BASED VACCINE DESIGN J. Biol. Chem., November 14, 2008; 283(46): 31279 - 31283. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. D. Lima and D. Reverter Structure of the Human SENP7 Catalytic Domain and Poly-SUMO Deconjugation Activities for SENP6 and SENP7 J. Biol. Chem., November 14, 2008; 283(46): 32045 - 32055. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Anand, I. Pallares, Z. Valnickova, T. Christensen, J. Vendrell, K. U. Wendt, H. A. Schreuder, J. J. Enghild, and F. X. Aviles The Crystal Structure of Thrombin-activable Fibrinolysis Inhibitor (TAFI) Provides the Structural Basis for Its Intrinsic Activity and the Short Half-life of TAFIa J. Biol. Chem., October 24, 2008; 283(43): 29416 - 29423. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Milic, T. V. Demidkina, N. G. Faleev, D. Matkovic-Calogovic, and A. A. Antson Insights into the Catalytic Mechanism of Tyrosine Phenol-lyase from X-ray Structures of Quinonoid Intermediates J. Biol. Chem., October 24, 2008; 283(43): 29206 - 29214. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Mori, K. Kitano, S.-i. Terawaki, R. Maesaki, Y. Fukami, and T. Hakoshima Structural Basis for CD44 Recognition by ERM Proteins J. Biol. Chem., October 24, 2008; 283(43): 29602 - 29612. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Islam, S. Sohya, K. Noguchi, M. Yohda, and Y. Kuroda Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines PNAS, October 7, 2008; 105(40): 15334 - 15339. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Vila, J. M. Aramini, P. Rossi, A. Kuzin, M. Su, J. Seetharaman, R. Xiao, L. Tong, G. T. Montelione, and H. A. Scheraga Quantum chemical 13C{alpha} chemical shift calculations for protein NMR structure determination, refinement, and validation PNAS, September 23, 2008; 105(38): 14389 - 14394. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. A. Springer, J. Zhu, and T. Xiao Structural basis for distinctive recognition of fibrinogen {gamma}C peptide by the platelet integrin {alpha}IIb{beta}3 J. Cell Biol., August 25, 2008; 182(4): 791 - 800. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Fox III, I. Le Trong, P. Rajagopal, P. S. Brzovic, R. E. Stenkamp, and R. E. Klevit Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences J. Biol. Chem., July 25, 2008; 283(30): 21179 - 21186. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Sanchez-Moreno, R. Coral-Vazquez, J.P. Mendez, and P. Canto Full-length SRY protein is essential for DNA binding Mol. Hum. Reprod., June 1, 2008; 14(6): 325 - 330. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Sendamarai, R. S. Ohgami, M. D. Fleming, and C. M. Lawrence Structure of the membrane proximal oxidoreductase domain of human Steap3, the dominant ferrireductase of the erythroid transferrin cycle PNAS, May 27, 2008; 105(21): 7410 - 7415. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sheoran, G. Sharma, and E. A. First Activation of D-Tyrosine by Bacillus stearothermophilus Tyrosyl-tRNA Synthetase: 1. PRE-STEADY-STATE KINETIC ANALYSIS REVEALS THE MECHANISTIC BASIS FOR THE RECOGNITION OF D-TYROSINE J. Biol. Chem., May 9, 2008; 283(19): 12960 - 12970. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Michalska, A. Hernandez-Santoyo, and M. Jaskolski The Mechanism of Autocatalytic Activation of Plant-type L-Asparaginases J. Biol. Chem., May 9, 2008; 283(19): 13388 - 13397. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. X. Weichenberger, P. Byzia, and M. J. Sippl Visualization of unfavorable interactions in protein folds Bioinformatics, May 1, 2008; 24(9): 1206 - 1207. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Richardson, B. Schneider, L. W. Murray, G. J. Kapral, R. M. Immormino, J. J. Headd, D. C. Richardson, D. Ham, E. Hershkovits, L. D. Williams, et al. RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution) RNA, March 1, 2008; 14(3): 465 - 481. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Richards, K. A. Johnson, H. Liu, A.-M. McRobbie, S. McMahon, M. Oke, L. Carter, J. H. Naismith, and M. F. White Structure of the DNA Repair Helicase Hel308 Reveals DNA Binding and Autoinhibitory Domains J. Biol. Chem., February 22, 2008; 283(8): 5118 - 5126. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Severi, A. Muller, J. R. Potts, A. Leech, D. Williamson, K. S. Wilson, and G. H. Thomas Sialic Acid Mutarotation Is Catalyzed by the Escherichia coli {beta}-Propeller Protein YjhT J. Biol. Chem., February 22, 2008; 283(8): 4841 - 4849. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Mallorqui-Fernandez, S. P. Manandhar, G. Mallorqui-Fernandez, I. Uson, K. Wawrzonek, T. Kantyka, M. Sola, I. B. Thogersen, J. J. Enghild, J. Potempa, et al. A New Autocatalytic Activation Mechanism for Cysteine Proteases Revealed by Prevotella intermedia Interpain A J. Biol. Chem., February 1, 2008; 283(5): 2871 - 2882. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. W. Barb, L. Jiang, C. R. H. Raetz, and P. Zhou Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: Time-dependent inhibition and specificity in ligand binding PNAS, November 20, 2007; 104(47): 18433 - 18438. [Abstract] [Full Text] [PDF]
|
|