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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.


Two distinct binding modes of the PCNA/FEN1/DNA and 9∆-1-1/FEN1/DNA complex. A–B) Cartoon representations of PCNA and 9-1-1 binding to dsDNA, colored in blue for Rad9 and PCNA1, yellow for Hus1 and PCNA3 and green for Rad1 and PCNA2. The dsDNA phosphodiester groups and basic residues on the inner surface of PCNA and 9-1-1 are shown in gray spheres and red surfaces, respectively. Schematic representations of C) PCNA/FEN1 and D) 9∆-1-1(Rad1)/FEN1 interfaces and contacts. Secondary structure elements are shown for the FEN1 C-terminal tail in orange and sliding clamp (PCNA/Rad1) in blue. Ribbon representations of the core of FEN1 with secondary structure elements are labeled. Hydrophobic pockets on the PCNA surface are indicated in green. (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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f0015: Two distinct binding modes of the PCNA/FEN1/DNA and 9∆-1-1/FEN1/DNA complex. A–B) Cartoon representations of PCNA and 9-1-1 binding to dsDNA, colored in blue for Rad9 and PCNA1, yellow for Hus1 and PCNA3 and green for Rad1 and PCNA2. The dsDNA phosphodiester groups and basic residues on the inner surface of PCNA and 9-1-1 are shown in gray spheres and red surfaces, respectively. Schematic representations of C) PCNA/FEN1 and D) 9∆-1-1(Rad1)/FEN1 interfaces and contacts. Secondary structure elements are shown for the FEN1 C-terminal tail in orange and sliding clamp (PCNA/Rad1) in blue. Ribbon representations of the core of FEN1 with secondary structure elements are labeled. Hydrophobic pockets on the PCNA surface are indicated in green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Mentions: Detailed analysis of the contacts of clamp/DNA or clamp/FEN1 with the models has illuminated the structural basis for their functional specialties (Fig. 3). FEN1 adopts an overall upright position on the clamp's surface, with its DNA substrate passing through the ring at a tilted angle; in either case, the upstream DNA passes through the 9-1-1 ring at an even greater angle than it does through the PCNA ring. The DNA also forms more persistent contacts with the inner layer of clamp in 9-1-1/FEN1/DNA. The distinct DNA interactions with these clamp proteins are consistent with the functional difference between the two complexes: PCNA needs to be mobile on DNA in conjunction with replicative polymerases, while 9-1-1 serves as a temporary scaffold for DNA repair at specific sites. Interesting differences in the interactions of clamp/FEN1 for each complex were also observed beyond the conservative, inter-domain connector loop – PCNA-interacting protein motif (PIP) interaction, often referred to as “IDCL-PIP box interaction”. The PCNA/FEN1 interface features two stable hydrophobic pockets in the C-terminus of PCNA, which interact with the PIP box in the C-terminus of FEN1 (Fig. 3C). In contrast, the Rad1/FEN1 interface lacks the corresponding hydrophobic interactions (Fig. 3D). This difference rationalizes a previous report that the exact C-terminal residues responsible for stimulation of FEN1 by the two clamps are distinct [86].


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

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

Two distinct binding modes of the PCNA/FEN1/DNA and 9∆-1-1/FEN1/DNA complex. A–B) Cartoon representations of PCNA and 9-1-1 binding to dsDNA, colored in blue for Rad9 and PCNA1, yellow for Hus1 and PCNA3 and green for Rad1 and PCNA2. The dsDNA phosphodiester groups and basic residues on the inner surface of PCNA and 9-1-1 are shown in gray spheres and red surfaces, respectively. Schematic representations of C) PCNA/FEN1 and D) 9∆-1-1(Rad1)/FEN1 interfaces and contacts. Secondary structure elements are shown for the FEN1 C-terminal tail in orange and sliding clamp (PCNA/Rad1) in blue. Ribbon representations of the core of FEN1 with secondary structure elements are labeled. Hydrophobic pockets on the PCNA surface are indicated in green. (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

f0015: Two distinct binding modes of the PCNA/FEN1/DNA and 9∆-1-1/FEN1/DNA complex. A–B) Cartoon representations of PCNA and 9-1-1 binding to dsDNA, colored in blue for Rad9 and PCNA1, yellow for Hus1 and PCNA3 and green for Rad1 and PCNA2. The dsDNA phosphodiester groups and basic residues on the inner surface of PCNA and 9-1-1 are shown in gray spheres and red surfaces, respectively. Schematic representations of C) PCNA/FEN1 and D) 9∆-1-1(Rad1)/FEN1 interfaces and contacts. Secondary structure elements are shown for the FEN1 C-terminal tail in orange and sliding clamp (PCNA/Rad1) in blue. Ribbon representations of the core of FEN1 with secondary structure elements are labeled. Hydrophobic pockets on the PCNA surface are indicated in green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Mentions: Detailed analysis of the contacts of clamp/DNA or clamp/FEN1 with the models has illuminated the structural basis for their functional specialties (Fig. 3). FEN1 adopts an overall upright position on the clamp's surface, with its DNA substrate passing through the ring at a tilted angle; in either case, the upstream DNA passes through the 9-1-1 ring at an even greater angle than it does through the PCNA ring. The DNA also forms more persistent contacts with the inner layer of clamp in 9-1-1/FEN1/DNA. The distinct DNA interactions with these clamp proteins are consistent with the functional difference between the two complexes: PCNA needs to be mobile on DNA in conjunction with replicative polymerases, while 9-1-1 serves as a temporary scaffold for DNA repair at specific sites. Interesting differences in the interactions of clamp/FEN1 for each complex were also observed beyond the conservative, inter-domain connector loop – PCNA-interacting protein motif (PIP) interaction, often referred to as “IDCL-PIP box interaction”. The PCNA/FEN1 interface features two stable hydrophobic pockets in the C-terminus of PCNA, which interact with the PIP box in the C-terminus of FEN1 (Fig. 3C). In contrast, the Rad1/FEN1 interface lacks the corresponding hydrophobic interactions (Fig. 3D). This difference rationalizes a previous report that the exact C-terminal residues responsible for stimulation of FEN1 by the two clamps are distinct [86].

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.