Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM) and small angle X-ray scattering (SAXS) have opened up new avenues to...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2015-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037015000409 |
| _version_ | 1828779621912412160 |
|---|---|
| author | Xiaojun Xu Chunli Yan Robert Wohlhueter Ivaylo Ivanov |
| author_facet | Xiaojun Xu Chunli Yan Robert Wohlhueter Ivaylo Ivanov |
| author_sort | Xiaojun Xu |
| collection | DOAJ |
| description | While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM) and small angle X-ray scattering (SAXS) have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF) method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES) methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair. |
| first_indexed | 2024-12-11T17:05:00Z |
| format | Article |
| id | doaj.art-6ea5faa4376344babe362959354ba743 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-11T17:05:00Z |
| publishDate | 2015-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-6ea5faa4376344babe362959354ba7432022-12-22T00:57:43ZengElsevierComputational and Structural Biotechnology Journal2001-03702015-01-0113C49250310.1016/j.csbj.2015.08.005Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic ResolutionXiaojun XuChunli YanRobert WohlhueterIvaylo IvanovWhile conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM) and small angle X-ray scattering (SAXS) have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF) method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES) methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair.http://www.sciencedirect.com/science/article/pii/S2001037015000409Integrative modelingHybrid modelingMolecular dynamics flexible fitting (MDFF)Small angle X-ray scattering (SAXS)Electron microscopy (EM)DNA replication and repair |
| spellingShingle | Xiaojun Xu Chunli Yan Robert Wohlhueter Ivaylo Ivanov Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution Computational and Structural Biotechnology Journal Integrative modeling Hybrid modeling Molecular dynamics flexible fitting (MDFF) Small angle X-ray scattering (SAXS) Electron microscopy (EM) DNA replication and repair |
| title | Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution |
| title_full | Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution |
| title_fullStr | Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution |
| title_full_unstemmed | Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution |
| title_short | Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution |
| title_sort | integrative modeling of macromolecular assemblies from low to near atomic resolution |
| topic | Integrative modeling Hybrid modeling Molecular dynamics flexible fitting (MDFF) Small angle X-ray scattering (SAXS) Electron microscopy (EM) DNA replication and repair |
| url | http://www.sciencedirect.com/science/article/pii/S2001037015000409 |
| work_keys_str_mv | AT xiaojunxu integrativemodelingofmacromolecularassembliesfromlowtonearatomicresolution AT chunliyan integrativemodelingofmacromolecularassembliesfromlowtonearatomicresolution AT robertwohlhueter integrativemodelingofmacromolecularassembliesfromlowtonearatomicresolution AT ivayloivanov integrativemodelingofmacromolecularassembliesfromlowtonearatomicresolution |