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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.


Ub primarily adopts docked positions in PCNAK107-Ub while SUMO occupies extended positions in PCNAK164-SUMO (A,B) χ values for the triplet PCNAK107-Ub and PCNAK164-SUMO structures plotted against RMSD. Conformations selected by MES are highlighted in blue, magenta and red, respectively. (C,D) Overlaid SAXS profiles. (E,F) Overlaid P(r) plots. (G,H) The most populated atomic structures from MES analysis of PCNAK107-Ub and PCNAK164-SUMO in surface representation. The K107 and K164 attachment points are depicted in red. PCNA, Ub and SUMO are shown in gray, green and blue, respectively. (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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f0035: Ub primarily adopts docked positions in PCNAK107-Ub while SUMO occupies extended positions in PCNAK164-SUMO (A,B) χ values for the triplet PCNAK107-Ub and PCNAK164-SUMO structures plotted against RMSD. Conformations selected by MES are highlighted in blue, magenta and red, respectively. (C,D) Overlaid SAXS profiles. (E,F) Overlaid P(r) plots. (G,H) The most populated atomic structures from MES analysis of PCNAK107-Ub and PCNAK164-SUMO in surface representation. The K107 and K164 attachment points are depicted in red. PCNA, Ub and SUMO are shown in gray, green and blue, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Mentions: We have recently extended this work to provide a common hybrid modeling/SAXS framework and examined K107-Ub and SUMOylated PCNA [84]. The biological functions of the small ubiquitin-related modifier SUMO appear to be even more diverse, ranging from nuclear transport to signal transduction, transcription, and genome stability [85]. Sumoylation of PCNA occurs on two lysines, predominantly on K164 and to a lesser extent on K127. Attachment of SUMO can induce a variety of cellular outcomes but often its mode of action remains poorly understood. To explore the overall architecture and flexibility of yeast PCNAK107-Ub and PCNAK164-SUMO complexes, we examined solution conformations with small-angle X-ray scattering (SAXS). Yeast PCNAK107-Ub was produced using chemical cross-linking with a K107C mutant PCNA. The PCNAK164-SUMO complex was formed by split-fusion [76]. Experimental SAXS curves (Fig. 7), along with a compaction observed in the pair distribution P(r) plot, show the three complexes adopt conformations with different levels of compactness in solution. The χ fit of the SAXS model to existing crystal structures (with PDB codes 3L10 and 3V60) produced high values, consistent with significant discrepancies between the observed structures in solution and in the crystalline environment.


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

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

Ub primarily adopts docked positions in PCNAK107-Ub while SUMO occupies extended positions in PCNAK164-SUMO (A,B) χ values for the triplet PCNAK107-Ub and PCNAK164-SUMO structures plotted against RMSD. Conformations selected by MES are highlighted in blue, magenta and red, respectively. (C,D) Overlaid SAXS profiles. (E,F) Overlaid P(r) plots. (G,H) The most populated atomic structures from MES analysis of PCNAK107-Ub and PCNAK164-SUMO in surface representation. The K107 and K164 attachment points are depicted in red. PCNA, Ub and SUMO are shown in gray, green and blue, respectively. (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

f0035: Ub primarily adopts docked positions in PCNAK107-Ub while SUMO occupies extended positions in PCNAK164-SUMO (A,B) χ values for the triplet PCNAK107-Ub and PCNAK164-SUMO structures plotted against RMSD. Conformations selected by MES are highlighted in blue, magenta and red, respectively. (C,D) Overlaid SAXS profiles. (E,F) Overlaid P(r) plots. (G,H) The most populated atomic structures from MES analysis of PCNAK107-Ub and PCNAK164-SUMO in surface representation. The K107 and K164 attachment points are depicted in red. PCNA, Ub and SUMO are shown in gray, green and blue, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Mentions: We have recently extended this work to provide a common hybrid modeling/SAXS framework and examined K107-Ub and SUMOylated PCNA [84]. The biological functions of the small ubiquitin-related modifier SUMO appear to be even more diverse, ranging from nuclear transport to signal transduction, transcription, and genome stability [85]. Sumoylation of PCNA occurs on two lysines, predominantly on K164 and to a lesser extent on K127. Attachment of SUMO can induce a variety of cellular outcomes but often its mode of action remains poorly understood. To explore the overall architecture and flexibility of yeast PCNAK107-Ub and PCNAK164-SUMO complexes, we examined solution conformations with small-angle X-ray scattering (SAXS). Yeast PCNAK107-Ub was produced using chemical cross-linking with a K107C mutant PCNA. The PCNAK164-SUMO complex was formed by split-fusion [76]. Experimental SAXS curves (Fig. 7), along with a compaction observed in the pair distribution P(r) plot, show the three complexes adopt conformations with different levels of compactness in solution. The χ fit of the SAXS model to existing crystal structures (with PDB codes 3L10 and 3V60) produced high values, consistent with significant discrepancies between the observed structures in solution and in the crystalline environment.

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.