How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways 1 1Edited by J. Thornton

Lüdemann, Susanna K.; Lounnas, Valère; Wade, Rebecca C.

doi:10.1006/jmbi.2000.4155

Cited by 146 publications

(189 citation statements)

References 36 publications

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“…After the inhibitor crossed over the bottleneck, the aromatic ring of F108 completely flipped up. A similar phenomenon has also been observed in the SMD simulations on P450 101 with camphor (Ludemann et al, 2000b). In that simulation, the two phenylalanine residues F193 and F87 were flipped up for the substrate to exit the active site.…”

Section: Discussionsupporting

confidence: 77%

“…This channel is similar to channel 2 in the present study. Molecular dynamics simulations on both P450 102 (Paulsen and Ornstein, 1995;Chang and Loew, 1999) and P450 101 (Ludemann et al, 2000b) demonstrated that residues at the mouth of this channel underwent a conformational change. As a result, the width of the mouth of this channel was slightly larger than its value in the crystal structures, which readily allows a ligand to pass through.…”

Section: Discussionmentioning

confidence: 99%

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Possible Pathway(s) of Metyrapone Egress from the Active Site of Cytochrome P450 3A4: A Molecular Dynamics Simulation

Liu²,

Luo³

et al. 2007

Drug Metab Dispos

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ABSTRACT:To identify a possible pathway(s) for metyrapone egress from the active site of P450 3A4, a 5-ns conventional molecular dynamics simulation followed by steered molecular dynamics simulations was performed on the complex with metyrapone. The steered molecular dynamics simulations showed that metyrapone egress via channel 1, threading through the B-C loop, only required a relatively small rupture force and small displacement of residues, whereas egress via the third channel, between helix I and helices F and G, required a relatively large force and perturbation of helices I, B, and C. The conventional dynamics simulation indicated that channel 2, located between the ␤1 sheet, B-B loop, and F-G region, is closed because of the movement of residues in the mouth of this channel. The findings suggest that channel 1 can be used for metyrapone egress, whereas both channel 2 and channel 3 have a low probability of serving as an exit channel for metyrapone. In addition, residues F108 and I120 appear to act as two gatekeepers to prevent the inhibitor from leaving the active site. These results are in agreement with previous site-directed mutagenesis experiments.

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Section: Discussionsupporting

confidence: 77%

Section: Discussionmentioning

confidence: 99%

Possible Pathway(s) of Metyrapone Egress from the Active Site of Cytochrome P450 3A4: A Molecular Dynamics Simulation

Liu²,

Luo³

et al. 2007

Drug Metab Dispos

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“…Sitedirected mutagenesis revealed that substitution of residues in the N-terminus of helix I can alter the activity and stereoselectivity of P450 2B1 (Scott et al, 2004a). Moreover, random repulsion molecular dynamics simulations have indicated a similar substrate egress pathway in P450CAM (Ludemann et al, 2000). In the current SMD simulation, the secondary structures of helices I and G are well maintained, and the rupture force is relatively small during testosterone exit along channel 1.…”

Section: Smd Simulation Of Testosterone Egress From P450 2b1mentioning

confidence: 67%

Possible Pathway(s) of Testosterone Egress From the Active Site of Cytochrome P450 2b1: A Steered Molecular Dynamics Simulation

Li¹,

Liu²,

Scott³

et al. 2005

Drug Metab Dispos

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ABSTRACT:To probe the possible substrate exit channel(s) in cytochrome P450 (P450) 2B1 and to clarify the role of residues previously identified by site-directed mutagenesis, a homology model was constructed based on the X-ray crystal structure of a P450 2B4-inhibitor complex. Testosterone was docked into the active site of P450 2B1 and was then pulled out through three putative channels using steered molecular dynamics simulations. The results indicated that of the three channels, the "solvent channel," lined by helices E, F, and I and the ␤3 hairpin, required the largest rupture force and backbone motion, which rendered it unlikely as an exit route. The relatively small rupture forces and backbone motions for the other two channels suggested them as possible candidates for testosterone passage. The opening of channel 1, located between helices G and I and the B-C loop, is characterized by rotation of the aromatic ring of Phe297 together with a bending of the B-C loop. The opening of channel 2, penetrating through the B-C loop/ B helix, is achieved by an expansion of this region and a small displacement of the backbone. Interestingly, during the egress of testosterone along channel 1, Phe297 and Phe108 appear to act as two clamps to stabilize testosterone binding and prevent it from leaving the active site. Phe115 acts as a gatekeeper for channel 2. These results are in agreement with previous sitedirected mutagenesis experiments.

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“…Several experimental and computational studies of enzymes with buried active sites, such as acetylcholinesterases (6,44), haloalkane dehalogenases (12,43), cytochromes P450 (7,18,45,46), and lipases (47)(48)(49)(50) have been performed and have underlined the importance of enzyme tunnels for catalytic activity, specificity, and enantioselectivity. Here, we report the first combined experimental and computational study of the effect of a tunnel-lining mutation on the mechanism of the biotechnologically interesting enzyme, haloalkane dehalogenase LinB.…”

Section: Discussionmentioning

confidence: 99%

A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB

Biedermannová

Prokop

Góra

et al. 2012

Journal of Biological Chemistry

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Background: Tunnel properties affect ligand passage in enzymes with buried active sites. Results: A tunnel mutation from leucine to tryptophan changes the mechanism of bromide ion release from haloalkane dehalogenase LinB. Conclusion:Interactions of the bromide ion with the tryptophan increase free energy barrier for its passage, causing the reaction mechanism change. Significance: The results provide guidelines for enzyme engineering.

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How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways 1 1Edited by J. Thornton

Cited by 146 publications

References 36 publications

Possible Pathway(s) of Metyrapone Egress from the Active Site of Cytochrome P450 3A4: A Molecular Dynamics Simulation

Possible Pathway(s) of Metyrapone Egress from the Active Site of Cytochrome P450 3A4: A Molecular Dynamics Simulation

Possible Pathway(s) of Testosterone Egress From the Active Site of Cytochrome P450 2b1: A Steered Molecular Dynamics Simulation

A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB

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