[3dem] De novo model building from medium-resolution cryo EM maps

[John Rubinstein]

Dear Grigory,

What you are trying to do can be challenging. However, we’ve had some success determining the fold of proteins where no homologous protein structures are known by combining information from evolutionary covariance analysis with cryo-EM maps at ~6 Å resolution. Have a look at these two examples:
http://www.ncbi.nlm.nih.gov/pubmed/26951669
http://www.ncbi.nlm.nih.gov/pubmed/26439008

For these two manuscripts (3 structures), Daniel Schep built the models manually and obtained evolutionary covariance (aka "evolutionary couplings") information from Deborah Marks’ program EVcouplings (http://evfold.org/evfold-web/newmarkec.do). Evolutionary covariance analysis works best when a large multiple sequence alignment for your protein of interest can be prepared. For example, for the bovine mitochondrial ATP synthase a subunit, where >20,000 sequences are available because of homology to bacterial ATP synthases, constraints on the fold from intra-chain contacts could be detected with excellent signal to noise. For the Thermus thermophilus and Saccharomyces cerevisiae V/A- and V-ATPases, only ~3000k sequences were available (eukaryotes, archaea, and a few eubacteria) and patterns of constraints were noisier but still easily detectable.

Best wises,
John

-- 
John Rubinstein
Molecular Structure and Function Program
The Hospital for Sick Children Research Institute
686 Bay Street, Rm. 20-9705
Toronto, ON
Canada
M5G 0A4
Tel: (+001) 416-813-7255
Fax: (+001) 416-813-5022
www.sickkids.ca/research/rubinstein

> On May 23, 2016, at 12:16 PM, Grigory Sharov <sharov.grigory at GMAIL.COM> wrote:
> 
> Dear all,
> 
> I'm looking for a software tool for de novo model building (no homologous structures available) based on a medium resolution density maps (5-8 A). The idea is to get at least a C-alpha trace and map it onto known protein sequence. 
> 
> So far I tried Gorgon and e2pathwalker from EMAN2 without much luck and now looking into Rosetta (not sure it is suitable for my resolution). I wonder what other people are using for such task.
> 
> 
> Best regards,
> Grigory
> 
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
> Institute of Genetics and Molecular and Cellular Biology
> Integrated Structural Biology Department (CBI)
> 1, rue Laurent Fries
> 67404 Illkirch, France
> tel. 03 69 48 51 00 <tel:03%2069%2048%2051%2000> 
> e-mail: sharov at igbmc.fr <mailto:sharov at igbmc.fr>_______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
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