[gmx-users] apoenzyme wanted

[Justin Lemkul]

On 9/24/14 1:36 PM, N. S. wrote:
> Dear Gromacs users,
>
> I study an enzyme (hydrolase), which is known to undergo some
> conformational changes upon substrate or inhibitor binding.
>
> Protein Data Bank at rcsb.org has only suitable entries with complex
> enzyme-inhibitor structures. I had got might be a stupid idea to make
> minimisation and then MD to obtain the apoenzyme conformation. I took out
> the ligand from the complex and prepared the protein for MD. I made the
> minimisation followed by one nanosecond production MD with Gromacs 4.5.5,

A simulation 1 ns in length is almost certainly an order of magnitude (or more) 
too short to convincingly identify any structural transitions that might occur. 
  The true time scale absolutely depends on the architecture of the protein, but 
I think 1 ns is too short for just about anything, especially if you went 
directly from minimization to production, because you have a large amount of 
frames that are unequilibrated.

> and now I have 9443 protein structures (frames).  I still have a reference,
> the main part of the apoenzyme missing a loop of 16 residues.
> Theoretically, one could superimpose each of 9443 structures to the
> truncated reference apoform one by one, and compare the distances between
> several residue C alpha atoms, and choose the best fitted structure among
> those 9443. However, you understand I won't do such a job. Could anybody
> supply me with a script, or better with a short line of code, to solve the
> problem. The problem is to fish out the structure, which is to be close to
> the native apoenzyme as much as possible? For now I will not care for the
> missing loop position. First I need to catch a golden fish from the pool
> populated with another similar 9442 fishes.
>

How does this help you identify the conversion to an apo form?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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