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Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution.

Xu X, Yan C, Wohlhueter R, Ivanov I - Comput Struct Biotechnol J (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, USA.

ABSTRACT
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.

No MeSH data available.


Flowchart of the modeling protocol for PCNAK164-Ub. (A) The strategy to generate models for PCNA with covalently bound ubiquitin. (B) The positions of the covalently bound Ub heavy atoms in 6837 frames from a 34-μs TBD simulation were binned and displayed relative to PCNA; the number of frames in each bin is color coded as from smallest (red) to largest (blue). (C) PCNAK164-Ub complex identified from multi-scale refinement in surface representation.
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f0025: Flowchart of the modeling protocol for PCNAK164-Ub. (A) The strategy to generate models for PCNA with covalently bound ubiquitin. (B) The positions of the covalently bound Ub heavy atoms in 6837 frames from a 34-μs TBD simulation were binned and displayed relative to PCNA; the number of frames in each bin is color coded as from smallest (red) to largest (blue). (C) PCNAK164-Ub complex identified from multi-scale refinement in surface representation.

Mentions: To examine the conformational space of Ub on PCNA more systematically, a successive, computational modeling approach was adopted by combining tethered Brownian dynamics (TBD) [91], protein–protein docking (using RosettaDock [92–94]), flexible loop modeling (using ModLoop [95,96]), and MD simulation (Fig. 5). First, an extensive TBD simulation of 34 μs identified a bound state of PCNA-Ub, based on electrostatic and shape complementarity. The resulting conformational ensemble was then clustered into 90 clusters in order to select the centroids for local protein–protein docking; in this process side-chain packing was allowed, as opposed to side-chain rigidity imposed in TBD. The distinct, dominant docking modes from the top three Rosetta-scoring models showed Ub situated in the large cleft defined by a β-sheet that forms the subunit–subunit interface of PCNA. As the tethering peptide in both TBD and RosettaDock calculations was included implicitly, the models were then completed by including the linker (Ub residues 72–76) into the structures obtained from clustering with RosettaDock (Fig. 5) using Modloop, and subsequently refined through ~ 25 ns all-atom, explicit solvent MD simulations.


Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution.

Xu X, Yan C, Wohlhueter R, Ivanov I - Comput Struct Biotechnol J (2015)

Flowchart of the modeling protocol for PCNAK164-Ub. (A) The strategy to generate models for PCNA with covalently bound ubiquitin. (B) The positions of the covalently bound Ub heavy atoms in 6837 frames from a 34-μs TBD simulation were binned and displayed relative to PCNA; the number of frames in each bin is color coded as from smallest (red) to largest (blue). (C) PCNAK164-Ub complex identified from multi-scale refinement in surface representation.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588362&req=5

f0025: Flowchart of the modeling protocol for PCNAK164-Ub. (A) The strategy to generate models for PCNA with covalently bound ubiquitin. (B) The positions of the covalently bound Ub heavy atoms in 6837 frames from a 34-μs TBD simulation were binned and displayed relative to PCNA; the number of frames in each bin is color coded as from smallest (red) to largest (blue). (C) PCNAK164-Ub complex identified from multi-scale refinement in surface representation.
Mentions: To examine the conformational space of Ub on PCNA more systematically, a successive, computational modeling approach was adopted by combining tethered Brownian dynamics (TBD) [91], protein–protein docking (using RosettaDock [92–94]), flexible loop modeling (using ModLoop [95,96]), and MD simulation (Fig. 5). First, an extensive TBD simulation of 34 μs identified a bound state of PCNA-Ub, based on electrostatic and shape complementarity. The resulting conformational ensemble was then clustered into 90 clusters in order to select the centroids for local protein–protein docking; in this process side-chain packing was allowed, as opposed to side-chain rigidity imposed in TBD. The distinct, dominant docking modes from the top three Rosetta-scoring models showed Ub situated in the large cleft defined by a β-sheet that forms the subunit–subunit interface of PCNA. As the tethering peptide in both TBD and RosettaDock calculations was included implicitly, the models were then completed by including the linker (Ub residues 72–76) into the structures obtained from clustering with RosettaDock (Fig. 5) using Modloop, and subsequently refined through ~ 25 ns all-atom, explicit solvent MD simulations.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, USA.

ABSTRACT
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.

No MeSH data available.