Subject: summary: template, NMR or X-ray

From: "Jianhui Wu" <[email-masked]>
Date: Fri, 03 Nov 2000 14:57:40 -0500

Dear All,

Early this week I asked a general question regarding homology modelling.
I received a lot of very helpful respond. I would like to thank Drs.
P.I.W. de. Bakker, M.R. Donkey, M. Forster, S. Cross, V. Mathura and J.
Gomar for their help.

The quality of the crystal struture and the sequence similarity between
the target and the templates are key factors to be considered. NMR
structure reflect the flexible part of the structure. It is hard to tell
whether the model from X-ray or NMR will be better. I intend to use the
model to do some database screen and the compounds with top score will
be synthesized and subject to biological assay. In other word, the model
(and probably me ) have to face the music really soon. As suggested, I
will try to build two models (one from NMR, the other one from X-ray)
since the sequence similarity between the target and template is about
the same in both case. I will use some active compounds as the control
in the docking. If nothing active in the end,  chemistry guy might
...... .   Oops, kind of scaring.

Best regards,

Yours sincerely,

Jian Hui Wu

PS: Please find my original question and the responds as follows
(text were edited due to broken lines).

***********Original question*********************************
> I have a general question regarding homology modelling. I would like to
> build a protein model for docking study. This protein have two close
> homology proteins (A and B) with their structures solved: A from X-ray
> and B from NMR. I wonder which template I should use? or perhaps I 
  should use two of them at the same time? What kind of template will 
  produce better protein model if we try to judge the model by the 
  docking result as well as the biological experimental result. It 
  seems that NMR structure will be more in accord with what is going 
  on in solution. Can we say that model built by template from NMR will
  give a better result in docking study? Let`s assume the docking method
  and biological assay method are reasonable here. Any help will be 
  grateful appreciated.

**************Responds********************************

(1) "P.I.W. de Bakker" <[email-masked]>

That very much depends on two things:
(a) What is the quality of the crystal structure (its resolution)? In
comparative modelling people tend to prefer the x-tal structure to the
NMR structure. However, if the x-tal structure is, let's say 3.0 A
resolution, then the NMR might be a better template.

(b) Just as important, what's the similarity of your target sequence to
both the NMR and X-ray structure?  If your target sequence is much more
distant to the Xray structure then too you should use the NMR structure.

If your target is an obvious homologue (>50% PID) then take the highest
quality template. That you're using the comparative model for docking
studies should in this regard not matter.

Yours,

Paul
*****************************************
(2) Mr Donkey <[email-masked]>

Jianhui,

First let me start by saying, I have NOT come across anything in the
literature that says as a general rule that an NMR struct or X-ray
struct will give better homology modeling results.
Many modeling studies have been done, using X-ray and NMR structures.

>From the homology modeling viewpoint, X-ray has the advantage of only
offering 1 structure, whereas NMR structures are deposited in an
ensemble of conformers, all of which satisfy the restarings derived from
the experiments. So this presents another problem/decision in the 
homology modeling process - which conformer(s) will you use? 
or maybe an average structure?

As you suggested, you can also use a combination of templates.

The most important factor in choosing the templates is the sequence
identity; I don't think experimental technique plays any role in this
decision.

hope this helps

- don
**************************************************
(3) Mark Forster <[email-masked]>

Dear Jianhui Wu

In such a situation you can use two template molecules. Several programs
support such a facility (Modeller is one such program). Distance
constraints derived from both structures can be used in a single 
penalty function for optimisation. The relative weights of the 
constraints from the two structures will depend on the local similarity
between the template and query sequence.

Mark

********************************************************
(4)  Simon Cross <[email-masked]>

Hello, I build homology models of antibodies and use purely crystal
structures and loop grafting before minimising. However, if NMR
structures were available then I would tend to use them more
as it is a more accurate representation in solution, as you have said.
The model you build can never be proven to be 100% accurate, so as 
long as you realise the limitations inherent in the method then it's ok. 
Why not try to construct two models, one from X-ray, one from NMR and 
compare the two? If you get a docked structure just from NMR then
it will be interesting, as maybe the binding site exists in the 
'closed' form in the crystal structure. Any interaction is just a 
'possible' so don't try to draw concrete conclusions.

Hope this helps,

Simon Cross
University of Nottingham
UK

****************************************************
(5) Venkat Mathura <[email-masked]>

hi,

   if this question is about making just the models than I would say go
ahead with template structure determined by X-ray (provided its of high
resolution).  But, if I am correct, you want to build a multimer. In
that case I would suggest build models with both x-ray and NMR templates
(do compare the templates itself to understand where exactly the 
differences are). Then try to dock  with both the models (provided 
if it is not a very tedious process!).  The reason for that is X-ray 
structures is just one, and NMR structures (although bundled , sometimes
averaged) of course do represent the solution state. So each has its 
own benefit. Your aim will be to dock molecules without problem.  If
both the models (based on X-ray and NMR ) are good, than just X-ray 
result will be fine.

In short,

  1. consider X-ray struct resolution
  2. consider the xray and nmr struc difference
  3. consider xray or nmr struc if multimeric struc is already available
(who knows while docking there may be conformational changes, so as a
safe bet its better to use similarly docked or multimeric structure)
  4. evaluate your models based on both templates
  5. which ever you find good will be the one you want
  6. if both are good x-ray will be fine,

all the best

venkat
*********************************************
(6) Jerome Gomar <[email-masked]>

Dear Jianhui,

Your homology modeling problem can be splitted in two issues :

1/ which reference structure should you choose ?
The answer is in the % of sequence homology between your target ( the
protein to be modelled) and your template ( protein A and/or B).
More precisely, the local sequence homology (calculated on a segment
part of the sequence) could give you some indication of structurally
conserved regions ( sequence homology is a necessary condition for
structural similarity). This % of homology could give you an indication
of the weight of the 3D information coming from protein A or B that you
need to build the homology model.

2/ What kind of information could you get from NMR ?
NMR structures will give you some additional usefull indication on the
flexibility of some part of the structure, in the loops for example. If
you are performing some docking, this kind of information is important.
To my point of view, you should consider the average minimized NMR
structure as your template B.

Hope this help.

Regards

Jérôme
*********************************************************
E.O.F.