for some examples of one way to do these calculations, see our publications
listed below where we did this type of calculation using Amber:
*DNA Deformation-Coupled Recognition of 8‑Oxoguanine: Conformational
Kinetic Gating in Human DNA Glycosylase *
Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman,
Dmitry O. Zharkov, and Carlos Simmerling, Journal of the American Chemical
Society, 2017, 139 (7), 2682-2692
DOI: 10.1021/jacs.6b11433
*A Dynamic Checkpoint in Oxidative Lesion Discrimination by
Formamidopyrimidine–DNA Glycosylase*
Li, H., Endutkin, A., Bergonzo, C., Grollman, A.; Campbell, A., de los
Santos, C., Zharkov, D., Simmerling, C., Nucleic Acids Research,
2015,44(2), 683-94
DOI:10.1093/nar/gkv1092
*Rational modulation of the induced-fit conformational change for
slow-onset inhibition in M. tuberculosis InhA*
Lai, C-T., Li, H; Yu, W., Shah, S., Bommineni, G., Perrone, V.,
Garcia-Diaz, M., Tonge, P., Simmerling, C., Biochemistry, 2015, 54 (30),
4683-4691
DOI: 10.1021/acs.biochem.5b00284
*Active destabilization of base pairs by a DNA glycosylase wedge initiates
damage recognition*
Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V.,
de los Santos, C., Grollman, A. P., Fedorova, O. S., Zharkov, D. O.,
Simmerling, C., Nucleic Acids Research, 2015, 43 (1), 272-281
DOI: 10.1093/nar/gku1300
*A structural and energetic model for the slow-onset inhibition of the
Mycobacterium tuberculosis enoyl-ACP reductase InhA*
Li, H.; Lai, C.; Pan, P.; Yu, W.; Liu, N.; Bommineni, G.; Garcia-Diaz, M.;
Simmerling, C. .; Tonge, PJ., ACS Chemical Biology, 2014, 9, (4), 986–993
DOI: 110.1021/cb400896g
*Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase*
Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling,
C., Journal of the American Chemical Society, 2011, 133, 14504–14506
DOI: 10.1021/ja205142d
On Wed, Jun 21, 2017 at 9:02 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Jun 20, 2017, waleed zalloum wrote:
>
> > I have simulated an enzyme, and I found that it has two different
> > conformers. I want to find the free energy path between them and find if
> > there is a transition state between these two conformers.
>
> This is one of those questions that is way too general to have any easy
> answer. In general, this is a very hard problem, and depends a lot on the
> nature of the barrier between the conformers.
>
> Broadly speaking, you need to find some collective ("progress") variable(s)
> that describe the change between the conformers. Then the methods
> described
> in Chap. 21 of the Reference Manual may help.
>
> In some cases, you may be able to use the methods described in Chap 20,
> without needing to identify collective variables.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 23 2017 - 07:00:02 PDT
