Study of the Behavior of Lysozyme Oligomers in Solutions by the Molecular Dynamics Method

被引：14
作者：
Kordonskaya, Yu. V. [1 ]
Timofeev, V. I. [1 ,2 ]
Dyakova, Yu. A. [1 ,2 ]
Marchenkova, M. A. [1 ,2 ]
Pisarevsky, Yu. V. [1 ,2 ]
Podshivalov, D. D. [1 ,2 ,3 ]
Kovalchuk, M. V. [1 ,2 ,4 ]
机构：
[1] Russian Acad Sci, Shubnikov Inst Crystallog, Fed Sci Res Ctr Crystallog & Photon, Moscow 119333, Russia
[2] Natl Res Ctr, Kurchatov Inst, Moscow 123182, Russia
[3] Moscow MV Lomonosov State Univ, Moscow 119991, Russia
[4] St Petersburg State Univ, St Petersburg 199034, Russia
来源：
CRYSTALLOGRAPHY REPORTS | 2018年 / 63卷 / 06期
基金：
俄罗斯基础研究基金会;
关键词：
INITIAL CRYSTALLIZATION STAGE; X-RAY-SCATTERING; PROTEIN;
D O I：
10.1134/S1063774518060196
中图分类号：
O7 [晶体学];
学科分类号：
0702 ; 070205 ; 0703 ; 080501 ;
摘要：
The dynamics of octamers of two types, which form (via translation) a tetragonal lysozyme crystal lattice, has been simulated on a 100-ns path with and without a precipitant. It is shown that one of the octamers under study is stable in the presence of a precipitant, whereas the other octamer dissociates into components both in the presence and in the absence of a precipitant. The results obtained not only confirmed the results of previous measurements of lysozyme solutions with NaCl precipitant by small-angle X-ray neutron scattering but also made it possible to establish the type of the octamer forming in the crystallization solution.
引用
收藏
页码：947 / 950
页数：4
相关论文
共 23 条
[1]   Structural insights into the broad substrate specificity of carboxypeptidase T from Thermoactinomyces vulgaris [J].
Akparov, Valery Kh ;
Timofeev, Vladimir I. ;
Khaliullin, Ilyas G. ;
Svedas, Vytas ;
Chestukhina, Galina G. ;
Kuranova, Inna P. .
FEBS JOURNAL, 2015, 282 (07) :1214-1224
[2]  
Boiko K. M., 2015, USP KHIM, V84, P853, DOI [10.1070/RCR4557, DOI 10.1070/RCR4557]
[3]   Small-angle X-ray scattering study of the influence of solvent replacement (from H2O to D2O) on the initial crystallization stage of tetragonal lysozyme [J].
Boikova, A. S. ;
D'yakova, Yu. A. ;
Il'ina, K. B. ;
Konarev, P. V. ;
Kryukova, A. E. ;
Marchenkova, M. A. ;
Blagov, A. E. ;
Pisarevskii, Yu. V. ;
Koval'chuk, M. V. .
CRYSTALLOGRAPHY REPORTS, 2017, 62 (06) :837-842
[4]   Octamer formation in lysozyme solutions at the initial crystallization stage detected by small-angle neutron scattering [J].
Boikova, Anastasiia S. ;
Dyakova, Yulia A. ;
Ilina, Kseniia B. ;
Konarev, Petr V. ;
Kryukova, Alyona E. ;
Kuklin, Alexandr I. ;
Marchenkova, Margarita A. ;
Nabatov, Boris V. ;
Blagov, Alexandr E. ;
Pisarevsky, Yurii V. ;
Kovalchuk, Mikhail V. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2017, 73 :591-599
[5]   Design, Synthesis, and Biological Evaluation of Novel 2H-Pyran-2-one Derivatives as Potential HIV-1 Reverse Transcriptase Inhibitors [J].
Defant, Andrea ;
Mancini, Ines ;
Tomazzolli, Rossella ;
Balzarini, Jan .
ARCHIV DER PHARMAZIE, 2015, 348 (01) :23-33
[6]   PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations [J].
Dolinsky, TJ ;
Nielsen, JE ;
McCammon, JA ;
Baker, NA .
NUCLEIC ACIDS RESEARCH, 2004, 32 :W665-W667
[7]   Small-Angle X-ray Scattering Study of Conditions for the Formation of Growth Units of Protein Crystals in Lysozyme Solutions [J].
Dyakova, Yu. A. ;
Ilina, K. B. ;
Konarev, P. V. ;
Kryukova, A. E. ;
Marchenkova, M. A. ;
Blagov, A. E. ;
Volkov, V. V. ;
Pisarevsky, Yu. V. ;
Kovalchuk, M. V. .
CRYSTALLOGRAPHY REPORTS, 2017, 62 (03) :364-369
[8]   Features and development of Coot [J].
Emsley, P. ;
Lohkamp, B. ;
Scott, W. G. ;
Cowtan, K. .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 :486-501
[9]   A historical perspective on protein crystallization from 1840 to the present day [J].
Giege, Richard .
FEBS JOURNAL, 2013, 280 (24) :6456-6497
[10]   COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER [J].
JORGENSEN, WL ;
CHANDRASEKHAR, J ;
MADURA, JD ;
IMPEY, RW ;
KLEIN, ML .
JOURNAL OF CHEMICAL PHYSICS, 1983, 79 (02) :926-935
123