[ccp4bb] Intra-molecular interactions

2012-11-03 Thread Xiaodi Yu

Dear All:

I have a quick question: how common it is that electrostatic interactions are 
involved in intra-molecular interactions, particularly in intrinsically 
disordered proteins? Is this interaction specific and any example?

Thanks,

Dee

Xiaodi Yu, Ph.D.
Boston Children's Hospital 
Dana-Farber Cancer Institute
Harvard Medical School
3 Blackfan
Boston, MA 02115
  

Re: [ccp4bb] Intra-molecular interactions

2012-11-03 Thread Chittaranjan Das
Dee,

Intramolecular electrostatic interactions are common in protein structures, for 
example between i and i+4 pairs on the same face of a helix. Robert Baldwin 
(Stanford) and others did a lot of work on the contribution of intramolecular 
salt bridges to helix stabilization in model helices. If I remember correctly, 
some of his studies indicated that disrupting the ionic interaction could 
completely destabilize the helix.
 
Your real question is if they play a role in disordered regions. The way I 
think about this is that an intramolecular salt bridge may be able to induce 
structure in an otherwise disordered region (if the pairs are strategically 
located). Alternatively, the entropic penally of folding may be too much to pay 
for by the enthalpy gain due to such an interaction (remember solvation).

The bottom line is that the fact that it is disordered means the interaction is 
not contributing significantly.  

Chitta




 

- Original Message -
From: Xiaodi Yu uppsala@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Saturday, November 3, 2012 12:06:32 PM
Subject: [ccp4bb] Intra-molecular interactions


Dear All: 

I have a quick question: how common it is that electrostatic interactions are 
involved in intra-molecular interactions, particularly in intrinsically 
disordered proteins? Is this interaction specific and any example? 

Thanks, 

Dee 

Xiaodi Yu, Ph.D. 
Boston Children's Hospital  
Dana-Farber Cancer Institute 
Harvard Medical School 
3 Blackfan 
Boston, MA 02115 


Re: [ccp4bb] Intra-molecular interactions

2012-11-03 Thread Ed Pozharski

On 11/03/2012 12:06 PM, Xiaodi Yu wrote:
how common it is that electrostatic interactions are involved in 
intra-molecular interactions, particularly in intrinsically disordered 
proteins?
It's impossible to answer your question unless you define what you mean 
by degree of commonality.


If you are asking if salt bridges happen - yes, they do.  All the time.

On the other hand, it must be impossible to conclude anything with 
certainty about details of interactions within intrinsically disordered 
proteins.  It's impossible to determine their structure because they 
are, well, disordered.  But I know of no law of physics that would 
prevent electrostatic interactions in such molecules.


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs



Re: [ccp4bb] Intra-molecular interactions

2012-11-03 Thread Petri Kursula
For some starting points, google electrostatic interactions in intrinsically 
disordered proteins. Of course they occur in IDPs; they even have 
proportionally more charged residues than folded proteins. 

Petri

On Nov 3, 2012, at 5:06 PM, Xiaodi Yu wrote:

 Dear All:
 
 I have a quick question: how common it is that electrostatic interactions are 
 involved in intra-molecular interactions, particularly in intrinsically 
 disordered proteins? Is this interaction specific and any example?
 
 Thanks,
 
 Dee
 
 Xiaodi Yu, Ph.D.
 Boston Children's Hospital 
 Dana-Farber Cancer Institute
 Harvard Medical School
 3 Blackfan
 Boston, MA 02115
 
 


---
Petri Kursula, PhD
Group Leader, Docent of Neurobiochemistry
Department of Biochemistry  Biocenter Oulu, University of Oulu, Finland
Department of Chemistry, University of Hamburg, Germany
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---



Re: [ccp4bb] graphical problems with coot 0.7

2012-11-03 Thread Paul Emsley

On 02/11/12 00:59, Michaela Renner-schneck wrote:

Hi,

I just upgraded from coot 0.6.2 to 0.7 - the stand alone package for 
running on mac os x 10.8.
While 0.6.2 is running perfectly well with the XQartz environment 0.7. 
totally messes up the graphical display of the model...




Relevant?

Coot FAQ 3.4:

http://www.biop.ox.ac.uk/coot/doc/coot-faq.html#I-get-bizarre-connectivity-and-other-weirdness-on-reading-files