From owner-biophys@hgmp.mrc.ac.uk Sun Sep 22 03:42:48 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 7727217A5E for ; Sun, 22 Sep 2002 03:42:47 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C24BC17AC7 for ; Sun, 22 Sep 2002 03:42:45 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D480A17A5E for ; Sun, 22 Sep 2002 03:42:43 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA03602 for biophys-list@hgmp.mrc.ac.uk; Sun, 22 Sep 2002 03:42:43 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: bbruner@uclink4.berkeley.edu (Bob) X-Newsgroups: bionet.biophysics Subject: Re: Ends of sequence critical to tertiary structure too? Date: Sun, 22 Sep 2002 02:41:57 GMT Organization: University of California, Berkeley Lines: 37 Message-ID: <3d8d2cf0.5266758@agate.berkeley.edu> References: <85160b48.0209180945.389b152@posting.google.com> X-Complaints-To: usenet@agate.berkeley.edu X-Newsreader: Forte Free Agent 1.2/16.242 To: biophys@hgmp.mrc.ac.uk X-Razor-id: f701f987e773b830cee61ae5d4dd94b8fd833f39 Sender: owner-biophys@hgmp.mrc.ac.uk Precedence: bulk On Sat, 21 Sep 2002 03:43:09 +0000 (UTC), Adrian wrote: >saco@moon.yerphi.am (Saco) wrote in >news:85160b48.0209180945.389b152@posting.google.com: > >>> You know amino acid sequence probably totally determines into what >>> tertiary structure the protein folds. >> >> Besides amino acid sequence, environment (pH level, temperature, etc.) >> dictates tertiary structure too. > >Are there some PRECISE databases listing how conformation changes for >particular protein item/identity/sequence and, AS WELL, pH, temperature, and >other factors? >As far as the protein databank entries as I know (sorry for ignorance) >usually for each protein item entry only one 3D-strucure is presented. If >this is not correct, please, provide me with some link! > If you go thru the databases in detail, there are some proteins for which there are multiple structures -- perhaps for mutants. Not much info. You won't find much vs pH, etc; the challenge is to get protein crystals at all for x-ray structure, so people are not choosy about the conditions. Some of the best info might simply be for those proteins for which extensive mutational analysis has been done, such as the lac repressor protein of E. coli. For such a protein, there will be much info on which mutations have what activity. There will (generally) not be structures for each (too much work), but with a base structure, it may be possible to make inferences. bob .