[gmx-users] Re: Folding rate
bharat gupta
bharat.85.monu at gmail.com
Wed Jan 4 02:35:39 CET 2012
Thanks for all your replies. I want to know this can be done in gromacs or
not - using REMD with structure based models generated from SMOG server to
study protein folding and unfolding ??. Also, I have a question about how
to determine the exchange probablities for a particular REMD experiment
and also how many replicas do we need to consider, does that depend on the
temperature list generated from the T_REMD server??
On Sat, Dec 31, 2011 at 11:36 AM, felmerino at uchile.cl
<felmerino at uchile.cl>wrote:
> Yeah sure. There are several methods to trick your peptide to fold, but
> often you loose the real kinetics by using them. I think a 230 residues
> protein is too big to study folding kinetics through MD (because of the
> folding kinetics, not the size of the system). With topology based
> potenitials (Go-like models) you surely can do it, but take into account
> the the core asumption there is that the energy landscape of your peptide
> is perfectly funneled to the native state, which is a very good
> approximation for small protein (like a 100 residues) but not so nice for
> bigger proteins. In fact, even small proteins have intermediate states
> which makes the energy landscape somehow rugged (the engrailed homeodomain,
> the trp repressor, etc). Besides that, it is not a trivial task to go from
> the reduced representation to real kinetic constants. Maybe if you are
> interested in comparison rather than absolute values you can be lucky with
> the Go-modeling. If that is the case maybe you should try the SMOG
> potential.... it is very fast.
>
>
>
> regards
>
> ----Mensaje original----
> De: bharat.85.monu at gmail.com
> Fecha: 30-dic-2011 22:45
>
> Para: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Asunto: Re: [gmx-users] Re: Folding rate
>
> The protein that I am dealing with is a 230 amino acid protein. I have
> come across some methods that used reduced space model of protein such as
> CABS for locating the protein folding pathway. An another paper describes
> about using Go model together with Rigid body dynamics for finding protein
> folding pathway.
>
> On Sat, Dec 31, 2011 at 10:23 AM, felmerino at uchile.cl <felmerino at uchile.cl
> > wrote:
>
>> I small thing to consider with that particular paper is that DE Shaw has
>> a special machine (Anton) to do those calculations, so in principle it is
>> not possible to reproduce them (in a reasonable amount of time) on a
>> regular (super)computer. I think your best shot, if your protein is small
>> enough, is to use accelerated MD mixed with some good old kramer's theory.
>> See for example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581.
>>
>> In any case it seems to me like too much of an effort, in the end here
>> you really rely in the accuracy of the forcefield.
>>
>> Regards
>>
>>
>> ----Mensaje original----
>> De: jmdamas at itqb.unl.pt
>> Fecha: 30-dic-2011 21:40
>> Para: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
>> Asunto: Re: [gmx-users] Re: Folding rate
>>
>>
>> As it was pointed out, the literature is vast on this subject.
>>
>>
>> Moreover, calculating folding rates from simulations is not a trivial
>> subject, and it relies on many assumptions (e.g. what is considered
>> "folded", that the sampling obtained is enough). Even for small peptides,
>> "enough sampling" may mean several hundreds of microsseconds, something not
>> accessible to everyone.
>>
>> For a very recent article on the subject, check out:
>>
>> Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How
>> Fast-Folding Proteins Fold, *Science* 334:517-520.
>> http://dx.doi.org/10.1126/science.1208351
>>
>> Regards,
>> João
>>
>> On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi <ksr at chemistry.umass.edu>wrote:
>>
>>> As Justin pointed out, there is a vast literature on this topic, you
>>> need to ask yourself what you seek, and look at many review articles to
>>> find some reasonable starting points for you own needs and designs. Beyond
>>> that, it's a lot of hard work...
>>>
>>> On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
>>>
>>> Thanks for your advice... Could you please refer me some papers
>>> regarding this ....
>>>
>>> On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi <ksr at chemistry.umass.edu>wrote:
>>>
>>>> No, there is no way to use such data to determine the folding rate of
>>>> the intact protein. If you used a fragment approach you could potentially
>>>> (read lots of papers on REMD) isolate nucleation sites, but minus the
>>>> tertiary interaction scheme you could not tell a compelling story. Now, if
>>>> you want to find nucleation sites and see if there are spatially proximal
>>>> sites and simulate them together... You might begin to tell a story.
>>>>
>>>> Ken
>>>>
>>>>
>>>> On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
>>>>
>>>>
>>>>>
>>>>> bharat gupta wrote:
>>>>>
>>>>>> Thanks for your reply. I want to whether does it make any sense or is
>>>>>> it possible to simulate fragments of proteins and find their folding rate
>>>>>> and then correlate it to folding rate of whole protein ??
>>>>>>
>>>>>
>>>>> Simulating arbitrary parts of a protein may or may not produce any
>>>>> relevant information, likely the latter. Independently folding domains
>>>>> might be simulated in isolation, but if there is a chance that the peptide
>>>>> sequences have any effect on neighboring residues or even more distal
>>>>> sites, you'll never produce anything useful.
>>>>>
>>>>> -Justin
>>>>>
>>>>> On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>>>>> jalemkul at vt.edu>> wrote:
>>>>>> bharat gupta wrote:
>>>>>> Hi,
>>>>>> I want to know whether it's possible to calculate the folding
>>>>>> rate of 20 residue peptide folding into a beta-hairpin using
>>>>>> gromacs ??
>>>>>> Anything is possible ;) But seriously, there is existing literature
>>>>>> on such topics, I suspect you can find methodology that will suit
>>>>>> your needs.
>>>>>> -Justin
>>>>>> -- ==============================__==========
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> MILES-IGERT Trainee
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>>>>>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>> ==============================__==========
>>>>>> -- gmx-users mailing list gmx-users at gromacs.org
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>>>>>> --
>>>>>> Bharat
>>>>>> Ph.D. Candidate
>>>>>> Room No. : 7202A, 2nd Floor
>>>>>> Biomolecular Engineering Laboratory
>>>>>> Division of Chemical Engineering and Polymer Science
>>>>>> Pusan National University
>>>>>> Busan -609735
>>>>>> South Korea
>>>>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>>>>> Mobile no. - 010-5818-3680
>>>>>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>>>>>
>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> MILES-IGERT Trainee
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>> ========================================
>>>>> --
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>>>
>>>
>>>
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
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>>
>>
>>
>> --
>> João M. Damas
>> PhD Student
>> Protein Modelling Group
>> ITQB-UNL, Oeiras, Portugal
>> Tel:+351-214469613
>>
>>
>>
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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
>
>
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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