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Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

Wells SA, van der Kamp MW, McGeagh JD, Mulholland AJ - PLoS ONE (2015)

Bottom Line: In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant.In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative.Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Bath, Bath, United Kingdom.

ABSTRACT
Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.

No MeSH data available.


Structures obtained from geometric simulations of flexible motion biased along different normal mode directions (mode 7+8 in red–see text, mode 8 in blue) and MD simulations (light green) that are most similar to (A) the asymmetric structure (gray; PDB ID: 1XMM) and (B) the chain-swapped asymmetric structure (gray).C) Cα RMSDs to the symmetric (1XML) and asymmetric (1XMM) crystal structures for every 100th frame of the flexible motion simulations along mode 8 (blue) and mode 8+7 (red).
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pone.0133372.g003: Structures obtained from geometric simulations of flexible motion biased along different normal mode directions (mode 7+8 in red–see text, mode 8 in blue) and MD simulations (light green) that are most similar to (A) the asymmetric structure (gray; PDB ID: 1XMM) and (B) the chain-swapped asymmetric structure (gray).C) Cα RMSDs to the symmetric (1XML) and asymmetric (1XMM) crystal structures for every 100th frame of the flexible motion simulations along mode 8 (blue) and mode 8+7 (red).

Mentions: On visual inspection of trajectories of flexible motion for 1XML, it is immediately apparent that motion biased parallel to mode 8 causes the N-terminal domain to tilt so that the active site closes (the beta hairpin carrying Asp111 approaches the helix carrying Trp175 on the C-terminal domain). This produces a structure quite similar to the 1XMM crystal structure; however, this flexible motion generates a "B-A" site rather than an "A-B" site, that is, the structure closes on the opposite side to that seen in the 1XMM crystal structure.[1] Fig 3B shows an overlay of a frame from this flexible motion with the "swapped-1XMM" structure; the Cα RMSD between the structures is 2.5 Å (see Fig 3C). This demonstrates that, firstly, the constraint network in the 1XML structure allows enough flexible motion for the structure to move directly to a 1XMM-like structure; and secondly, that the asymmetric cooperative motion involved in forming an active site is an intrinsic feature of the largely symmetric 1XML structure.


Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

Wells SA, van der Kamp MW, McGeagh JD, Mulholland AJ - PLoS ONE (2015)

Structures obtained from geometric simulations of flexible motion biased along different normal mode directions (mode 7+8 in red–see text, mode 8 in blue) and MD simulations (light green) that are most similar to (A) the asymmetric structure (gray; PDB ID: 1XMM) and (B) the chain-swapped asymmetric structure (gray).C) Cα RMSDs to the symmetric (1XML) and asymmetric (1XMM) crystal structures for every 100th frame of the flexible motion simulations along mode 8 (blue) and mode 8+7 (red).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4524684&req=5

pone.0133372.g003: Structures obtained from geometric simulations of flexible motion biased along different normal mode directions (mode 7+8 in red–see text, mode 8 in blue) and MD simulations (light green) that are most similar to (A) the asymmetric structure (gray; PDB ID: 1XMM) and (B) the chain-swapped asymmetric structure (gray).C) Cα RMSDs to the symmetric (1XML) and asymmetric (1XMM) crystal structures for every 100th frame of the flexible motion simulations along mode 8 (blue) and mode 8+7 (red).
Mentions: On visual inspection of trajectories of flexible motion for 1XML, it is immediately apparent that motion biased parallel to mode 8 causes the N-terminal domain to tilt so that the active site closes (the beta hairpin carrying Asp111 approaches the helix carrying Trp175 on the C-terminal domain). This produces a structure quite similar to the 1XMM crystal structure; however, this flexible motion generates a "B-A" site rather than an "A-B" site, that is, the structure closes on the opposite side to that seen in the 1XMM crystal structure.[1] Fig 3B shows an overlay of a frame from this flexible motion with the "swapped-1XMM" structure; the Cα RMSD between the structures is 2.5 Å (see Fig 3C). This demonstrates that, firstly, the constraint network in the 1XML structure allows enough flexible motion for the structure to move directly to a 1XMM-like structure; and secondly, that the asymmetric cooperative motion involved in forming an active site is an intrinsic feature of the largely symmetric 1XML structure.

Bottom Line: In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant.In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative.Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Bath, Bath, United Kingdom.

ABSTRACT
Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.

No MeSH data available.