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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.


Active orientation of DNA editing enzymes revealed in models of FEN1 with sliding clamps and DNA. Computational models of FEN1 with PCNA and 9-1-1 were developed based on one of the stabilized positions of FEN1 in a DNA-free PCNA crystal structure. Modeling revealed that the sliding clamps tilted the DNA toward FEN1. The PCNA and 9Δ-1-1 complexes are shown as cartoons. PCNA is shown in green, FEN1 in purple, Rad1 in green, Hus1 in yellow, Rad 9 in blue, and DNA in black. The gray surfaces are the FEN1/DNA from the original starting models. The surfaces for the two clamps in the starting models were omitted for clarity. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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f0005: Active orientation of DNA editing enzymes revealed in models of FEN1 with sliding clamps and DNA. Computational models of FEN1 with PCNA and 9-1-1 were developed based on one of the stabilized positions of FEN1 in a DNA-free PCNA crystal structure. Modeling revealed that the sliding clamps tilted the DNA toward FEN1. The PCNA and 9Δ-1-1 complexes are shown as cartoons. PCNA is shown in green, FEN1 in purple, Rad1 in green, Hus1 in yellow, Rad 9 in blue, and DNA in black. The gray surfaces are the FEN1/DNA from the original starting models. The surfaces for the two clamps in the starting models were omitted for clarity. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Mentions: The modeling process was started by overlaying FEN1 from the FEN1/DNA structure (PDB access code 3Q8L) and PCNA/FEN1 structure (PDB access code 1UL1). A double-stranded B-form DNA (dsDNA) extension was then introduced on the 3′ flap side to pass through the PCNA ring. An initial model of 9-1-1/FEN1/DNA was then generated by replacing PCNA in PCNA/FEN1/DNA with 9-1-1. FEN1 interacts with the Rad1 subunit in this complex based on previous experimental evidence. Both initial models were then refined through ~ 120 ns MD simulation to fully relax the systems, followed by pairwise RMSD clustering analysis to select the centroid of each dominant cluster as final model, shown in Fig. 1.


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

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

Active orientation of DNA editing enzymes revealed in models of FEN1 with sliding clamps and DNA. Computational models of FEN1 with PCNA and 9-1-1 were developed based on one of the stabilized positions of FEN1 in a DNA-free PCNA crystal structure. Modeling revealed that the sliding clamps tilted the DNA toward FEN1. The PCNA and 9Δ-1-1 complexes are shown as cartoons. PCNA is shown in green, FEN1 in purple, Rad1 in green, Hus1 in yellow, Rad 9 in blue, and DNA in black. The gray surfaces are the FEN1/DNA from the original starting models. The surfaces for the two clamps in the starting models were omitted for clarity. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

f0005: Active orientation of DNA editing enzymes revealed in models of FEN1 with sliding clamps and DNA. Computational models of FEN1 with PCNA and 9-1-1 were developed based on one of the stabilized positions of FEN1 in a DNA-free PCNA crystal structure. Modeling revealed that the sliding clamps tilted the DNA toward FEN1. The PCNA and 9Δ-1-1 complexes are shown as cartoons. PCNA is shown in green, FEN1 in purple, Rad1 in green, Hus1 in yellow, Rad 9 in blue, and DNA in black. The gray surfaces are the FEN1/DNA from the original starting models. The surfaces for the two clamps in the starting models were omitted for clarity. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Mentions: The modeling process was started by overlaying FEN1 from the FEN1/DNA structure (PDB access code 3Q8L) and PCNA/FEN1 structure (PDB access code 1UL1). A double-stranded B-form DNA (dsDNA) extension was then introduced on the 3′ flap side to pass through the PCNA ring. An initial model of 9-1-1/FEN1/DNA was then generated by replacing PCNA in PCNA/FEN1/DNA with 9-1-1. FEN1 interacts with the Rad1 subunit in this complex based on previous experimental evidence. Both initial models were then refined through ~ 120 ns MD simulation to fully relax the systems, followed by pairwise RMSD clustering analysis to select the centroid of each dominant cluster as final model, shown in Fig. 1.

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.