Re: Avoiding alpha-helix distortions

From: Chris Harrison (
Date: Sun Jul 06 2008 - 07:52:41 CDT


This is a larger question. If the sulphate is present in the
physiologic system then you should include it. If it is not and is
only present in the crystal then you must determine (comb the
literature) if the sulfate induces a conformational shift of the
protein ensemble that makes it more amenable to aggregation /
crystallization. However, I would suggest that you carefully examine
the literature for other ions that might serve the same role as the
sulfate before immediately assuming the crystal structure exhibits a
different conformation from that seen in solution. NMR structures of
the protein, if available, would be particularly helpful in this


On Sat, Jul 5, 2008 at 12:38 AM, Praveen Agrawal
<> wrote:
> Eric, I have a further query on the ion modeling with Protein. I am
> dealing with a protein which has sulphate ion and the crystallization
> paper says that the sulphates were added to make the protein
> 'amenable' to crystallization process. So, does this mean that while
> doing MD, I should take 'this' sulphate explicitly?
> Regards,
> Praveen
> On Wed, Jul 2, 2008 at 9:11 PM, Eric H. Lee <> wrote:
>> I agree with Peter. Something else to check for is whether the crystal
>> structure contains an artificial constraint like heavy metal ions which may
>> coordinate various parts of your protein together. Whether you end up
>> modeling these ions (or even seemingly innocuous elements such as crystal
>> waters) as part of your simulation makes a difference.
>> -Eric
>> On Jul 2, 2008, at 7:59 AM, Peter Freddolino wrote:
>> If you're willing to grab the cvs version of namd, you can use the
>> extrabonds feature (discussed previously:
>> to
>> constrain the backbone dihedrals of the helix. You have to set up the
>> extrabonds file, but this shouldn't take more than a simple script in vmd.
>> Constraining the backbone hydrogen bonds, the dihedrals, or both all seem to
>> work in my experience. However, you may want to try to understand more
>> clearly *why* the helices are distorting, before you apply external forces
>> to prevent it. If the force field is saying they should distort, there must
>> be some reason -- one should be careful in defining what is "correct" for
>> secondary structures if they're in an environment that seems to destabilize
>> what you expect.
>> Best,
>> Peter
>> Valeria Losasso wrote:
>> Hi all,
>> my question is the following: in my protein I have three long interacting
>> alpha helices. First of all I minimized the side chains by blocking the
>> backbone through a constant force. Nevertheless, if I try to minimize the
>> entire protein (since the previous step is clearly not enough to start a
>> dynamics) I get a series of distortions in the backbone of the helices,
>> probably due to their length and position.
>> The point is: is there an "automated" way to keep the secondary structure
>> with the correct parameters (dihedral angles and so on) - I mean: a way to
>> say "I want a standard alpha helix from residue X to residue Y"?
>> Or I have to setup manually all needed restraints among all atoms involved?
>> And in this second case, is it more convenient to restraint the hydrogen
>> bonds length or dihedral values or what?
>> Best regards,
>> Valeria Losasso
>> Eric H. Lee
>> Medical Scholars Program
>> Theoretical and Computational Biophysics Group, UIUC

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 Voice: 217-244-1733 Fax: 217-244-6078

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