Multi-scale calculation and global-fit analysis of hydrodynamic properties of biological macromolecules: determination of the overall conformation of antibody IgG molecules

被引：8
作者：
Amoros, D. [1 ]
Ortega, A. [1 ]
Harding, S. E. [2 ]
Garcia de la Torre, J. [1 ]
机构：
[1] Univ Murcia, Dept Quim Fis, Fac Quim, E-30071 Murcia, Spain
[2] Univ Nottingham, Natl Ctr Macromol Hydrodynam, Sch Biosci, Loughborough LE12 5RD, Leics, England
来源：
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS | 2010年 / 39卷 / 03期
关键词：
Multisubunit structure; HYDROSUB; Global fit analysis; HYDROFIT; Antibodies; GLOBULAR-PROTEINS; RIGID MACROMOLECULES; COMPUTER-PROGRAM; NMR RELAXATION; X-RAY; PREDICTION; PARTICLES; CRYSTALLOHYDRODYNAMICS; COEFFICIENTS; SCATTERING;
D O I：
10.1007/s00249-008-0388-7
中图分类号：
Q6 [生物物理学];
学科分类号：
071011 ;
摘要：
We present a scheme, based on existing and newly developed computational tools, for the determination of the overall conformation of biological macromolecules composed by domains or subunits, using from such structural determination easily available solution properties. In a multi-scale approach, atomic-level structures are used to provide simple shapes for the subunits, which are put together in a coarse grained model, with a few parameters that determine the overall shape of the macromolecule. Computer programs, like those in the HYDRO suite that evaluate the properties of either atomic or coarse-grained models. In this paper we present a new scheme for a global fit of multiple properties, implemented in a new computer program, HYDROFIT, which interfaces with the programs of the HYDRO suite to find an optimum, best-fitting structure in a robust but simple way. The determination of the overall structure of the native antibody IgG3, bearing a long hinge, and that of the hingeless mutant m15 is presented to test and confirm the validity of this simple, systematic and efficient scheme.
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收藏
页码：361 / 370
页数：10
相关论文
共 36 条
[11]   Hydrodynamic models and computational methods for NMR relaxation [J].
De La Torre, JG ;
Bernadó, P ;
Pons, M .
NUCLEAR MAGNETIC RESONANCE OF BIOLOGICAL MACROMOLECULES, PART C, 2005, 394 :419-430
[12]   Calculation of the solution properties of flexible macromolecules:: methods and applications [J].
de la Torre, JG ;
Sánchez, HE ;
Ortega, A ;
Hernández, JG ;
Fernandes, MX ;
Díaz, FG ;
Martínez, MCL .
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2003, 32 (05) :477-486
[13]  
de la Torre JG, 2002, BIOPOLYMERS, V63, P163
[14]   Calculation of hydrodynamic properties of globular proteins from their atomic-level structure [J].
de la Torre, JG ;
Huertas, ML ;
Carrasco, B .
BIOPHYSICAL JOURNAL, 2000, 78 (02) :719-730
[15]   HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images [J].
de la Torre, JG ;
Llorca, O ;
Carrascosa, JL ;
Valpuesta, JM .
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2001, 30 (06) :457-462
[16]   CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF A HUMAN FC FRAGMENT AND ITS COMPLEX WITH FRAGMENT-B OF PROTEIN-A FROM STAPHYLOCOCCUS-AUREUS AT 2.9-A AND 2.8-A RESOLUTION [J].
DEISENHOFER, J .
BIOCHEMISTRY, 1981, 20 (09) :2361-2370
[17]   SOLPRO: Theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles [J].
delaTorre, JG ;
Carrasco, B ;
Harding, SE .
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 1997, 25 (5-6) :361-372
[18]   HYDRO - A COMPUTER-PROGRAM FOR THE PREDICTION OF HYDRODYNAMIC PROPERTIES OF MACROMOLECULES [J].
DELATORRE, JG ;
NAVARRO, S ;
MARTINEZ, MCL ;
DIAZ, FG ;
CASCALES, JJL .
BIOPHYSICAL JOURNAL, 1994, 67 (02) :530-531
[19]   Calculation of hydrodynamic properties of small nucleic acids from their atomic structure [J].
Fernandes, MX ;
Ortega, A ;
Martínez, MCL ;
de la Torre, JG .
NUCLEIC ACIDS RESEARCH, 2002, 30 (08) :1782-1788
[20]   An analytical solution to the problem of the orientation of rigid particles by planar obstacles.: Application to membrane systems and to the calculation of dipolar couplings in protein NMR spectroscopy [J].
Fernandes, MX ;
Bernadó, P ;
Pons, M ;
de la Torre, JG .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2001, 123 (48) :12037-12047
1234