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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.


Related in: MedlinePlus

Comparison of geometric simulation and molecular dynamics trajectories of DcpS.1XML refers to the (approximately) symmetric structure (see Fig 1A), 1XMM to the assymetric structure (see Fig 1B) and 1XMM swapped to the asymmetric structure with swapped chain IDs. Plots of the Cα distance between Trp175 and Asp111’ for both actives sites (“AB” and “BA”) as observed in the flexible motion trajectories biased along modes 7, 8 and the linear combination of 7+8 (small closed symbols) and in the individual MD trajectories (crosses for every 100 ps); A) run 1, B) run 2, C) run 3, D) run 4.
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pone.0133372.g002: Comparison of geometric simulation and molecular dynamics trajectories of DcpS.1XML refers to the (approximately) symmetric structure (see Fig 1A), 1XMM to the assymetric structure (see Fig 1B) and 1XMM swapped to the asymmetric structure with swapped chain IDs. Plots of the Cα distance between Trp175 and Asp111’ for both actives sites (“AB” and “BA”) as observed in the flexible motion trajectories biased along modes 7, 8 and the linear combination of 7+8 (small closed symbols) and in the individual MD trajectories (crosses for every 100 ps); A) run 1, B) run 2, C) run 3, D) run 4.

Mentions: Here, we have extended our molecular dynamics investigation of DcpS to four independent trajectories of 100 ns each[21]. Fig 2 shows the range of intersite distances d(AB) and d(BA) explored during each of the MD runs (1–4), along with the ranges explored by the flexible motion simulations (see below). Different MD runs can display strikingly different behaviour in their exploration of the conformational space, with for example run 2 exploring mostly the symmetric closure motion while runs 1, 3 and 4 explore anti-symmetric motions in one direction (run 1) or both (runs 3,4). The extent of the motion during these longer MD trajectories naturally exceeds that explored in the previous study. The shortest active-site distance observed during asymmetric closure is d(AB) = 8.2 Å, while the shortest active-site distances achieved in a symmetric closure have d(AB) = d(BA)≈17 Å.


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)

Comparison of geometric simulation and molecular dynamics trajectories of DcpS.1XML refers to the (approximately) symmetric structure (see Fig 1A), 1XMM to the assymetric structure (see Fig 1B) and 1XMM swapped to the asymmetric structure with swapped chain IDs. Plots of the Cα distance between Trp175 and Asp111’ for both actives sites (“AB” and “BA”) as observed in the flexible motion trajectories biased along modes 7, 8 and the linear combination of 7+8 (small closed symbols) and in the individual MD trajectories (crosses for every 100 ps); A) run 1, B) run 2, C) run 3, D) run 4.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524684&req=5

pone.0133372.g002: Comparison of geometric simulation and molecular dynamics trajectories of DcpS.1XML refers to the (approximately) symmetric structure (see Fig 1A), 1XMM to the assymetric structure (see Fig 1B) and 1XMM swapped to the asymmetric structure with swapped chain IDs. Plots of the Cα distance between Trp175 and Asp111’ for both actives sites (“AB” and “BA”) as observed in the flexible motion trajectories biased along modes 7, 8 and the linear combination of 7+8 (small closed symbols) and in the individual MD trajectories (crosses for every 100 ps); A) run 1, B) run 2, C) run 3, D) run 4.
Mentions: Here, we have extended our molecular dynamics investigation of DcpS to four independent trajectories of 100 ns each[21]. Fig 2 shows the range of intersite distances d(AB) and d(BA) explored during each of the MD runs (1–4), along with the ranges explored by the flexible motion simulations (see below). Different MD runs can display strikingly different behaviour in their exploration of the conformational space, with for example run 2 exploring mostly the symmetric closure motion while runs 1, 3 and 4 explore anti-symmetric motions in one direction (run 1) or both (runs 3,4). The extent of the motion during these longer MD trajectories naturally exceeds that explored in the previous study. The shortest active-site distance observed during asymmetric closure is d(AB) = 8.2 Å, while the shortest active-site distances achieved in a symmetric closure have d(AB) = d(BA)≈17 Å.

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.


Related in: MedlinePlus