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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: 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.

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.


Symmetric (A) and asymmetric (B) forms of citrate synthase as generated by the geometric simulations (red, blue) biased along normal modes 9 (A) and 7 (B), started from the open structure (PDB ID: 3ENJ), compared to the closed structure (PDB ID: 2CTS, light gray).
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pone.0133372.g006: Symmetric (A) and asymmetric (B) forms of citrate synthase as generated by the geometric simulations (red, blue) biased along normal modes 9 (A) and 7 (B), started from the open structure (PDB ID: 3ENJ), compared to the closed structure (PDB ID: 2CTS, light gray).

Mentions: Fig 6A shows an overlay of the closed (2CTS) structure with a frame from geometric simulations biased along normal mode 9 of 3ENJ. It is clear that the motion captures the character of the crystallographically observed symmetric transition. Fig 6B, meanwhile, shows an overlay of the closed (2CTS) structure with a frame from geometric simulations biased along normal mode 7 of 3ENJ. In this case the alignment is carried out only on the closing chain of the dimer, chain A. We can see that the simulated closure of the binding cleft in chain A in this anti-symmetric motion appears to match the closed cleft of the 2CTS structure just as well as the symmetric motion does. The other cleft, meanwhile, has opened significantly beyond what is seen in "open" crystal structures of CS. Motions biased along mode 8 do not generate cleft geometries relevant for the open-closed transition as they show a different behaviour of the dihedral angle describing torsion of the dimer.


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)

Symmetric (A) and asymmetric (B) forms of citrate synthase as generated by the geometric simulations (red, blue) biased along normal modes 9 (A) and 7 (B), started from the open structure (PDB ID: 3ENJ), compared to the closed structure (PDB ID: 2CTS, light gray).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133372.g006: Symmetric (A) and asymmetric (B) forms of citrate synthase as generated by the geometric simulations (red, blue) biased along normal modes 9 (A) and 7 (B), started from the open structure (PDB ID: 3ENJ), compared to the closed structure (PDB ID: 2CTS, light gray).
Mentions: Fig 6A shows an overlay of the closed (2CTS) structure with a frame from geometric simulations biased along normal mode 9 of 3ENJ. It is clear that the motion captures the character of the crystallographically observed symmetric transition. Fig 6B, meanwhile, shows an overlay of the closed (2CTS) structure with a frame from geometric simulations biased along normal mode 7 of 3ENJ. In this case the alignment is carried out only on the closing chain of the dimer, chain A. We can see that the simulated closure of the binding cleft in chain A in this anti-symmetric motion appears to match the closed cleft of the 2CTS structure just as well as the symmetric motion does. The other cleft, meanwhile, has opened significantly beyond what is seen in "open" crystal structures of CS. Motions biased along mode 8 do not generate cleft geometries relevant for the open-closed transition as they show a different behaviour of the dihedral angle describing torsion of the dimer.

Bottom Line: 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.

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.