From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Sep 27 2007 - 16:34:20 CDT
I think sometimes what is philosophical to one is actually of interest to many; I myself am interested in things other than "just running software properly". Anyone can do that, it's understanding what's going on physically that is important.
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN
55414-2959
rwoodphd_at_yahoo.com
----- Original Message ----
From: Neema Salimi <nsalimi_at_msg.ucsf.edu>
To: namd-l_at_ks.uiuc.edu
Sent: Thursday, September 27, 2007 1:22:08 PM
Subject: Re: namd-l: Determining Transition State from an Unfolding Simulation
Hopefully this clears everything up.
Transition State: high energy state (maximum or saddle point on free energy surface)
Intermediate: metastable state (local minimum on free energy surface)
For protein folding, If one subscribes to transition state theory (or Kramer's theory), which has some shortcomings for protein folding, then a two-state folder (i.e. U <---> F) has no intermediates and one transition state TS. Many proteins have intermediates along the folding pathway (e.g. barnase), So in that case, you have U <---> I <---> F and two transition states, TS1 and TS2.
Structures of intermediates can be determined by varying reaction conditions to favor the intermediate, mutations, etc. (see Im7 from Sheena Radford's lab). Structures of the transition state cannot be observed directly and must be inferred from the reaction kinetics, normally of many mutants and other perturbations (e.g. phi-value analysis, psi-value analysis).
Computationally, some labs have had success identifying transition states using unfolding simulations and correlating those structures to kinetic data (e.g. phi values) of mutants.
And while I think this little discussion may be fruitful, it is not really germane to NAMD itself, and is much more of a scientific (and philosophical) question than one of properly running the software.
On Sep 27, 2007, at 9:22 AM, Richard Wood wrote:
Then I learned different kinetics.
What about A + B ------------->C?
|
| T1
| _
| / \
FE|\ / \
| \_/ \
| \_
| A+B C
|
|
|
|-------------------------->
Reaction pathway
Now, T1 is an intermediate and a transition state.
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
rwoodphd_at_yahoo.com
----- Original Message ----
From: Raymond C. Fort Jr. <rcfort_at_maine.edu>
To: Richard Wood <rwoodphd_at_yahoo.com>
Sent: Thursday, September 27, 2007 10:39:26 AM
Subject: Re: namd-l: Determining Transition State from an Unfolding Simulation
At 08:34 AM 9/27/2007, you wrote:
>Isn't an "intermediate" by definition a "transition state"? That's
>how I learned reaction kinetics.
>
>Richard
No. An intermediate is a minimum on the potential energy surface; a
transition state is a first order saddle point.
>Richard L. Wood, Ph. D.
>University of Minnesota
>Dept. of Medicinal Chemistry,
>College of Pharmacy
>717 Delaware St. SE
>Minneapolis, MN 55414-2959
>rwoodphd_at_yahoo.com
>
>---- Original Message ----
>From: paco ty <typaco_at_inbox.com>
>To: namd-l_at_ks.uiuc.edu
>Sent: Thursday, September 27, 2007 5:35:14 AM
>Subject: namd-l: Determining Transition State from an Unfolding Simulation
>
>I think Richard by "transition state" means more an "intermediate".
>
>
>
>
>Yahoo! oneSearch: Finally,
><http://us.rd.yahoo.com/evt=48252/*http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC>mobile
>search that gives answers, not web links.
Professor Ray Fort Jr. rcfort_at_maine.edu
Department of Chemistry chemistry.umeche.maine.edu/fort.html
University of Maine Voice: (207)-581-1180
Orono, ME 04469 FAX: (207)-581-1191
Computer modeling of organic and biomolecules; chemistry of lignin
and cellulose
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Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games.
Neema Salimi
nsalimi_at_msg.ucsf.edu
University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143
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