Insight into structural biophysics from solution X-ray scattering

被引:5
作者
Raviv, Uri [1 ,2 ]
Asor, Roi [1 ]
Shemesh, Asaf [1 ]
Ginsburg, Avi [1 ]
Ben-Nun, Tal [1 ]
Schilt, Yaelle [1 ]
Levartovsky, Yehonatan [1 ]
Ringel, Israel [3 ]
机构
[1] Hebrew Univ Jerusalem, Inst Chem, Edmond J Safra Campus, IL-9190401 Jerusalem, Israel
[2] Hebrew Univ Jerusalem, Ctr Nanosci & Nanotechnol, Edmond J Safra Campus, IL-9190401 Jerusalem, Israel
[3] Hebrew Univ Jerusalem, Inst Drug Res, Sch Pharm, IL-9112102 Jerusalem, Israel
基金
以色列科学基金会;
关键词
Self-assembly; SAXS; WAXS; Time-resolved SAXS; SMALL-ANGLE SCATTERING; DIRECT SHAPE DETERMINATION; D-PLUS SOFTWARE; BIOLOGICAL MACROMOLECULES; CALCIUM-IONS; WEB SERVER; HIERARCHICAL ALGORITHM; RESOLUTION STRUCTURE; MOLECULAR-DYNAMICS; SAXS;
D O I
10.1016/j.jsb.2023.108029
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The current challenges of structural biophysics include determining the structure of large self-assembled com-plexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystal-lography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
引用
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页数:21
相关论文
共 188 条
[1]   Upgrade of MacCHESS facility for X-ray scattering of biological macromolecules in solution [J].
Acerbo, Alvin Samuel ;
Cook, Michael J. ;
Gillilan, Richard Edward .
JOURNAL OF SYNCHROTRON RADIATION, 2015, 22 :180-186
[2]  
Als-Nielsen J., 2011, Elements of Modern X-ray Physics, V2nd
[3]   Bayesian inference of protein ensembles from SAXS data [J].
Antonov, L. D. ;
Olsson, S. ;
Boomsma, W. ;
Hamelryck, T. .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2016, 18 (08) :5832-5838
[4]   Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly [J].
Asor, Roi ;
Schlicksup, Christopher John ;
Zhao, Zhongchao ;
Zlotnick, Adam ;
Raviv, Uri .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2020, 142 (17) :7868-7882
[5]   pH stability and disassembly mechanism of wild-type simian virus 40 [J].
Asor, Roi ;
Khaykelson, Daniel ;
Ben-nun-Shaul, Orly ;
Levi-Kalisman, Yael ;
Oppenheim, Ariella ;
Raviv, Uri .
SOFT MATTER, 2020, 16 (11) :2803-2814
[6]   Assembly Reactions of Hepatitis B Capsid Protein into Capsid Nanoparticles Follow a Narrow Path through a Complex Reaction Landscape [J].
Asor, Roi ;
Selzer, Lisa ;
Schlicksup, Christopher John ;
Zhao, Zhongchao ;
Zlotnick, Adam ;
Raviv, Uri .
ACS NANO, 2019, 13 (07) :7610-7626
[7]   Effect of Calcium Ions and Disulfide Bonds on Swelling of Virus Particles [J].
Asor, Roi ;
Khaykelson, Daniel ;
Ben-nun-Shaul, Orly ;
Oppenheim, Ariella ;
Raviv, Uri .
ACS OMEGA, 2019, 4 (01) :58-64
[8]   Crystallization, Reentrant Melting, and Resolubilization of Virus Nanoparticles [J].
Asor, Roi ;
Ben-nun-Shaul, Orly ;
Oppenheim, Ariella ;
Raviv, Uri .
ACS NANO, 2017, 11 (10) :9814-9824
[9]  
Asor Roi., 2022, bioRxiv
[10]   Upgrade of D plus software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations [J].
Balken, Eytan ;
Ben-Nun, Itai ;
Fellig, Amos ;
Khaykelson, Daniel ;
Raviv, Uri .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2023, 56 :1295-1303