From chemistry-request@www.ccl.net Sun Jan 28 10:08:01 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id KAA10494; Sun, 28 Jan 1996 10:07:25 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id KAA16392 (8.6.11/IDA-1.6 for ); Sun, 28 Jan 1996 10:06:33 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id PAA09368; Sun, 28 Jan 1996 15:07:50 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id KAA16389 (8.6.11/IDA-1.6 for ); Sun, 28 Jan 1996 10:06:30 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id JAA10274; Sun, 28 Jan 1996 09:40:03 -0500 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id JAA10157; Sun, 28 Jan 1996 09:14:34 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA21800; Sun, 28 Jan 96 22:11:54 -0800 Date: Sun, 28 Jan 1996 22:11:53 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: CCL:Summary: Charges on protein Message-Id: Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Dear CCLers, About a week ago, I posted the question "Charge on proteins". Till now, I have got three answers --- they are proved to be very valuable. I am trying to compare these method now. Please feel free to express your opinion. My original question is: It is well known that the electrostatic interactions is one of the most important features in ligand-receptor binding. To calculate it, partial charges of both the ligand and the receptor (usually a protein molecule) are needed to be integrated into the Coulomb formula. If the ligand is a small, common organic molecule, relatively reliable values could be obtained by using semi-empirical algorithm. But the charges on the protein remain as a stumbling block. At present, many people use residue charge templates, which are derived from the quantum mechanical results of three peptides. The drawback of doing so is obvious. So my question is, is there any better way to get the partial charges on the protein? Any experience? Any ideas? Pointers to any literature are also appreciated. Here are the answers: ---------------------------------------------------------------------------- From: lou@scripps.edu (Lou Noodleman) Dear Arthur, We use PARSE charges due to Sitkoff,Sharp,Honig, J.Phys.Chem.1994,98, pages1978-1988, with good success. Lou Noodleman Molecular Biology The Scripps Research Institute La Jolla, CA 92037 ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- From: luciano@giotto (Luciano Brocchieri) Dear Arthur: I am not sure this is not what you don't want to use, but I feel comfortable with the AMBER forcefield. I can suggest to refer to Cornell et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J.Am.Chem.Soc., 117,5179-5197, and reference therein. Best wishes, Luciano Brocchieri (luciano@gnomic.stanford.edu) --------------------------------------------------------------------------- --------------------------------------------------------------------------- From: dopearso@magnus.acs.ohio-state.edu (Douglas C Pearson) the way that i've seen used most often (and have started using myself, in protein-protein docking problems) is one algorithm or another of assigning charges to residues through pKa calculations. usually this will involve (in its simplest form) placing formal charges on only the titrable atoms in the protein (oxygen atoms on carboxyls, nitrogen atoms on arginines, lysines and histidines, etc.), calculating a potential field over the whole atom, converting this potential field to pKa difference, and iterating the thing until you get constant pKa's over all residues after an iteration. you use the pKa to find the charge on each atom. my current favorite software of the moment, scott northrup's macrodox, uses the algorithm of matthew and gurd (methods in enzymology, 130:413). there are also articles from yang et. al. (proteins 15:252) and gilson (proteins 15:266...yes, these articles are in the same issue, back to back!) describing different viewpoints on the same subject. hope this helps. be sure to e-mail me if you need any further info... reply-to: dcp@hobbes.biosci.ohio-state.edu -- chuck pearson - dopearso@magnus.acs.ohio-state.edu osu biophysics program, daddy of amelia catherine pearson. *THIS ACCOUNT TO DIE SOON - STAY TUNED FOR DETAILS* ------------------------------------------------------------------------------- Regards, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/arthur/home.htm _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: arthur@csb0.IPC.PKU.EDU.CN -- Original Sender From: Address: arthur@ipc.pku.edu.cn CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From chemistry-request@www.ccl.net Sun Jan 28 14:23:04 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id OAA12829; Sun, 28 Jan 1996 14:19:26 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id OAA20005 (8.6.11/IDA-1.6 for ); Sun, 28 Jan 1996 14:18:34 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id TAA13997; Sun, 28 Jan 1996 19:19:51 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id OAA20002 (8.6.11/IDA-1.6 for ); Sun, 28 Jan 1996 14:18:32 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id OAA12741; Sun, 28 Jan 1996 14:08:39 -0500 Received: from ns2.tju.edu for lzw@pumba.JCI.TJU.EDU by www.ccl.net (8.6.10/950822.1) id NAA12608; Sun, 28 Jan 1996 13:52:47 -0500 Received: from pumba.JCI.TJU.EDU by ns2.tju.edu with SMTP id AA28841 (5.67a/IDA-1.4.4 for <@ns2.tju.edu:chemistry@www.ccl.net>); Sun, 28 Jan 1996 13:52:47 -0500 Received: by pumba.JCI.TJU.EDU (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA29284; Sun, 28 Jan 1996 14:01:55 -0500 Date: Sun, 28 Jan 1996 14:01:54 -0500 (EST) From: lzw To: chemistry@www.ccl.net Subject: CCL:summary of left-handed helix Message-Id: Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Dear CCLers, I have posted a questions on left-handed helix and got 2 answers. Many thanks to Abby Parrill and Frank Eisenmenger for their answers. My question is hi, dear netter, I met a problem on left-handed helix structure in proteins. I hope to know if there any sequence can form left-handed helix. If there are, I need the sequences. I will summary the results and post it. Thanks in advance. ------------------------------------------------------------------------ Zhaowen, Did you try searching the PDB for left-handed helices? I found some this way, unfortunately I do not know what the PDB entry numbers were. Good luck. __________________________________________________________ Abby Parrill Chemistry Department Artificial Intelligence in Chemistry Laboratory The University of Arizona abby@mercury.aichem.arizona.edu __________________________________________________________ ------------------------------------------------------------------------- Hi, if you consider stretches with phi around +60 as "left-handed helices" than I suggest to search the outputs of Kabsch & Sander's DSSP program (available in Sander group's section of the http://www.embl-heidelberg.de): look for H or G assignments and select those with positive phi. There is another much more abundant type of left-handed backbone structure which might be of interest for you: see Adzhubei & Sternberg, J. Mol. Biol. 229,472-493,1993. Cheers, Frank Eisenmenger +------------------------------------------------------------------------+ | Institute of Biochemistry | | Medical Faculty of the Humboldt University (Charite) | | | | Hessische Str. 3-4 | | 10115 Berlin, Germany | | | | Phone: +49-30-28468-612 or -239 FAX: +49-30-28468-600 | | E-mail: eisenmenger@rz.hu-berlin.de | +------------------------------------------------------------------------+ Zhaowen Luo ---------------------------- Voice: (215)922-8754 (Night) (215)955-4567 (Day) FAX: (215)923-2117 URL: http://www.jci.tju.edu/~zluo -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: lzw@pumba.JCI.TJU.EDU -- Original Sender From: Address: lzw@pumba.JCI.TJU.EDU CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html