Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/springer-journals/crystallization-in-microgravity-and-the-atomic-resolution-structure-of-HzOp40JyKP
References (41)
-
K. Vanommeslaeghe, Elizabeth Hatcher, Chayan Acharya, S. Kundu, Shijun Zhong, Jihyun Shim, E. Darian, Olgun Guvench, Pedro Lopes, I. Vorobyov, Alexander MacKerell (2009)
CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fieldsJournal of Computational Chemistry, 31
-
C. Schütte, A. Fischer, W. Huisinga, P. Deuflhard (1999)
A Direct Approach to Conformational Dynamics Based on Hybrid Monte CarloJournal of Computational Physics, 151
-
M. Parrinello, A. Rahman (1981)
Polymorphic transitions in single crystals: A new molecular dynamics methodJournal of Applied Physics, 52
-
B. Husic, V. Pande (2017)
Note: MSM lag time cannot be used for variational model selection.The Journal of chemical physics, 147 17
-
A. Lashkov, N. Zhukhlistova, S. Sotnichenko, Azat Gabdulkhakov, Al'bert Mikhailov (2010)
Structural basis for the mechanism of inhibition of uridine phosphorylase from Salmonella typhimuriumCrystallography Reports, 55
-
K. Katsumata, H. Tomioka, T. Sumi, S. Yamashita, M. Takagi, F. Kato, R. Nakamura, Y. Koyanagi, T. Aoki, K. Kato (2003)
Correlation between clinicopathologic factors and kinetics of metabolic enzymes for 5-fluorouracil given to patients with colon carcinoma by two different dosage regimensCancer Chemotherapy and Pharmacology, 51
-
R. McGibbon, V. Pande (2014)
Variational cross-validation of slow dynamical modes in molecular kinetics.The Journal of chemical physics, 142 12
-
I. W. Davis (2007)
10.1093/nar/gkm216Nucl. Acids Res., 35
-
P. Evans
Biological Crystallography Scaling and Assessment of Data Quality -
A. Lashkov, A. Gabdulkhakov, I. Prokofev, T. Seregina, S. Sotnichenko, A. Lyashenko, A. Shtil, A. Mironov, C. Betzel, A. Mikhailov (2012)
Expression, purification, crystallization and preliminary X-ray structure analysis of Vibrio cholerae uridine phosphorylase in complex with thymidine.Acta crystallographica. Section F, Structural biology and crystallization communications, 68 Pt 11
-
G. Pérez-Hernández, Fabian Paul, T. Giorgino, G. Fabritiis, F. Noé (2013)
Identification of slow molecular order parameters for Markov model construction.The Journal of chemical physics, 139 1
-
C. Wehmeyer, Martin Scherer, Tim Hempel, B. Husic, S. Olsson, F. Noé (2019)
Introduction to Markov state modeling with the PyEMMA software [Article v1.0]Living Journal of Computational Molecular Science
-
A. Vagin, A. Teplyakov (1997)
MOLREP: an Automated Program for Molecular ReplacementJournal of Applied Crystallography, 30
-
Jing Huang, Sarah Rauscher, G. Nawrocki, T. Ran, M. Feig, B. Groot, H. Grubmüller, A. MacKerell (2016)
CHARMM36m: an improved force field for folded and intrinsically disordered proteinsNature Methods, 14
-
(2007)
Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids -
P. Eistrikh-Heller, S. Rubinsky, I. Prokofev, A. Gabdulkhakov, A. Mironov, A. Lashkov (2020)
X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-AnhydrouridineCrystallography Reports, 65
-
J. Åqvist, J. Marelius (2001)
The linear interaction energy method for predicting ligand binding free energies.Combinatorial chemistry & high throughput screening, 4 8
-
A. Kanzaki, Y. Takebayashi, H. Bando, J. Eliason, Shin‐ichi Watanabe, H. Miyashita, M. Fukumoto, M. Toi, T. Uchida (2002)
Expression of uridine and thymidine phosphorylase genes in human breast carcinomaInternational Journal of Cancer, 97
-
P. Evans (2006)
10.1107/S0907444905036693Acta Crystallogr. D, 62
-
W. Kabsch (2010)
10.1107/S0907444909047337Acta Crystallogr. D, 66
-
A. Lashkov, N. Zhukhlistova, A. Gabdoulkhakov, A. Shtil, R. Efremov, C. Betzel, A. Mikhailov (2010)
The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution.Acta crystallographica. Section D, Biological crystallography, 66 Pt 1
-
P. Emsley, B. Lohkamp, William Scott, K. Cowtan (2010)
Features and development of CootActa Crystallographica Section D: Biological Crystallography, 66
-
C. Luccioni, J. Beaumatin, V. Bardot, D. Lefrançois (1994)
Pyrimidine nucleotide metabolism in human colon carcinomas: Comparison of normal tissues, primary tumors and xenograftsInternational Journal of Cancer, 58
-
D. Spoel, E. Lindahl, B. Hess, G. Groenhof, A. Mark, H. Berendsen (2005)
GROMACS: Fast, flexible, and freeJournal of Computational Chemistry, 26
-
P. Afonine, R. Grosse-Kunstleve, N. Echols, J. Headd, N. Moriarty, M. Mustyakimov, T. Terwilliger, A. Urzhumtsev, P. Zwart, P. Adams (2012)
Towards automated crystallographic structure refinement with phenix.refineActa Crystallographica Section D: Biological Crystallography, 68
-
I. Prokofev, A. Lashkov, A. Gabdulkhakov, V. Balaev, Alexander Mironov, Christian Betzel, A. Mikhailov (2018)
Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-MethyluracilCrystallography Reports, 63
-
I. Prokofev, A. Lashkov, A. Gabdulkhakov, M. Dontsova, T. Seregina, A. Mironov, C. Betzel, A. Mikhailov (2014)
Crystallization and preliminary X-ray study of Vibrio cholerae uridine phosphorylase in complex with 6-methyluracil.Acta crystallographica. Section F, Structural biology communications, 70 Pt 1
-
E. Snell, J. Helliwell (2005)
Macromolecular crystallization in microgravityReports on Progress in Physics, 68
-
Antonio Neto, Juliana Souza, L. Romanello, Alexandre Cassago, V. Serrão, R. DeMarco, J. Brandão-Neto, R. Garratt, H. Pereira (2016)
Analysis of two Schistosoma mansoni uridine phosphorylases isoforms suggests the emergence of a protein with a non-canonical function.Biochimie, 125
-
C. Schütte, W. Huisinga (2003)
Biomolecular Conformations can be Identified as Metastable Sets of Molecular DynamicsHandbook of Numerical Analysis, 10
-
W. Kabsch, C. Sander (1983)
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers, 22
-
K. Boyko, V. Timofeev, V. Samygina, I. Kuranova, Vladimir Popov, M. Kovalchuk (2016)
Protein crystallization under microgravity conditions. Analysis of the results of Russian experiments performed on the International Space Station in 2005−2015Crystallography Reports, 61
-
G. Bussi, M. Parrinello (2008)
Stochastic thermostats: comparison of local and global schemesComput. Phys. Commun., 179
-
T. Caradoc-Davies, S. Cutfield, I. Lamont, J. Cutfield (2004)
Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium.Journal of molecular biology, 337 2
-
Benjamin Trendelkamp-Schroer, Hao Wu, Fabian Paul, F. Noé (2015)
Estimation and uncertainty of reversible Markov models.The Journal of chemical physics, 143 17
-
Y. Abramchik, V. Timofeev, T. Muravieva, R. Esipov, I. Kuranova (2016)
Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9Crystallography Reports, 61
-
R. Hong, Y. Tseng (2003)
A phase II and pharmacokinetic study of pegylated liposomal doxorubicin in patients with advanced hepatocellular carcinomaCancer Chemotherapy and Pharmacology, 51
-
T. Roosild, S. Castronovo, A. Villoso, A. Ziemba, G. Pizzorno (2011)
A novel structural mechanism for redox regulation of uridine phosphorylase 2 activity.Journal of structural biology, 176 2
-
R. Laskowski, M. MacArthur, D. Moss, J. Thornton (1993)
PROCHECK: a program to check the stereochemical quality of protein structuresJournal of Applied Crystallography, 26
-
G. Bussi, T. Zykova-Timan, M. Parrinello (2009)
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling.The Journal of chemical physics, 130 7
-
Informatika
- Publisher
- Springer Journals
- Copyright
- Copyright © Pleiades Publishing, Inc. 2021. ISSN 1063-7745, Crystallography Reports, 2021, Vol. 66, No. 5, pp. 777–785. © Pleiades Publishing, Inc., 2021. Russian Text © The Author(s), 2021, published in Kristallografiya, 2021, Vol. 66, No. 5, pp. 750–758.
- ISSN
- 1063-7745
- eISSN
- 1562-689X
- DOI
- 10.1134/s1063774521050059
- Publisher site
- See Article on Publisher Site
Abstract
Uridine phosphorylases are known as key targets for the development of new anticancer and antiparasitic agents. Crystals of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae were grown in microgravity by the capillary counter-diffusion method on board of the International Space Station. The three-dimensional structure of this enzyme was determined at atomic (1.04 Å) resolution (RCSB PDB ID: 6Z9Z). Alternative conformations of long fragments (β-strands and adjacent loops) of the protein molecule were found for the first time in the three-dimensional structure of uridine phosphorylase in the absence of specific bound ligands. Apparently, these alternative conformations are related to the enzyme function. Conformational analysis with Markov state models demonstrated that conformational rearrangements can occur in the ligand-free state of the enzyme.
Journal
Crystallography Reports – Springer Journals
Published: Sep 1, 2021