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Hi, James, As we know, for oligomeric proteins, the interfaces are usually big and strong, and hydrophobic interaction contribute to their stability. It is difficult to be disrupted by solvent water or ions and their kd values are usually very small. For the small molecule, things may be different. The interchange rate between momomer and dimer or oligomer can be very fast in solution. In light of this, the oligomeric states of small molecule (cyclic di-nucleotides-CDNs) can not affect the enzymatic or binding activity of protein if CDNs are used as substrate or ligand. weiguo At 2016-01-24 15:41:13, "Deepak Thankappan Nair" <[log in to unmask]> wrote: My question: is the structure questionable or the challenge questionable? FYI challenge & response: http://www.nature.com/nature/journal/v437/n7057/full/nature04199.html biochemical verification of interpretation: http://www.ncbi.nlm.nih.gov/pubmed/16014707 structural verification of interpretation: http://www.ncbi.nlm.nih.gov/pubmed/16216587 independent group shows something similar: http://www.ncbi.nlm.nih.gov/pubmed/20961860 (there are more) there are more papers related to this topic from independent groups. to cut a long story short, the challenger decided that the space group is different, calculated maps in that space group and of course the maps were fuzzy. the challenge was published as a BCA in Nature based on one line from a referee "if Nair et al have got the space group wrong, they should set the record right immediately" the challenge and response were sent to this second referee after the challenger registered an appeal against the first referees decision that there were no problems with interpretation. Regarding sending structure factors/structure to reviewers, I would be afraid that somebody would steal the data, kill the paper and submit it themselves- especially if it is a close competitor. And yes, there are journals that will accept papers without a PDB submission. best Deepak On Sun, Jan 24, 2016 at 2:10 AM, Tom Peat <[log in to unmask]> wrote: It has been a very interesting discussion and one aspect that hasn't really been discussed has come to mind: the editor has to know that X or Y is a competitor, so if you as the author haven't put that in your letter to the editor, it falls back on your head. The editor has to find 2-3 reviewers that know the area well (usually the biology more than just the crystallography). And sometimes editors have a hard time finding that many people willing to review the papers. At a minimum, those publishing papers should be reviewing 3x the number of papers they publish- one for each reviewer and one for the editor (so if you publish 10 papers a year you should be reviewing 30). If you aren't, you aren't holding up your end of the bargain. cheers, tom Tom Peat Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 [log in to unmask] ________________________________________ From: CCP4 bulletin board [[log in to unmask]] on behalf of Mark J van Raaij [[log in to unmask]] Sent: Sunday, January 24, 2016 3:18 AM To: [log in to unmask] Subject: Re: [ccp4bb] questionable structures I¡¯m afraid I don¡¯t agree with Quyen - I do of course agree with the value of orthogonal methods (binding assays plus site-directed mutation of the residues involved in the binding site springs to mind in the case of ligand structures). Specifically, a competitor should not be reviewing your paper in the first place. He or she should not have been invited by the editor, and if invited, should have declined the invitation straight-away. I have almost always requested structure factors and coordinates when reviewing a structure paper, and they have always been provided without any questions or problems. I plan to continue asking for this in all future papers I review, and will refuse to review the paper if the authors do not provide them. When submitting a paper, I always try to provide the structure factors and coordinates upon submission as supplementary files not to be published, if the option is there. I also think the pdb should take a more active role in rooting out at least the most clearly erroneous structures, we need participation by the journals, pdb and reviewers. Which brings me to another point: have any ¡°structures¡± been published in predatory journals yet and submitted to the pdb? As these journals will accept anything virtually un-reviewed, only the pdb can prevent those structures contaminating the database. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://wwwuser.cnb.csic.es/~mjvanraaij > On 23 Jan 2016, at 15:42, Jurgen Bosch <[log in to unmask]> wrote: > > I agree with Quyen on both points. If you want to get your questionable structure published you better anticipate all questions a reviewer may have and stick them into the supplement in the first submission. Or add them as additional files for reviewer, which is often an option. > Orthogonal methods to X-ray crystallography - aka biochemistry or other biophysical experiments supporting your opinion have to be added. I'm thinking ITC, SPR, MST, enzyme kinetics, mass spec etc. > > In general it is wise to try to disprove your own result before trying to publish it, > > J¨¹rgen > > ...................... > J¨¹rgen Bosch > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://lupo.jhsph.edu > > On Jan 23, 2016, at 08:41, Quyen Hoang <[log in to unmask]> wrote: > >> I have mixed feelings about the idea of providing referees access to model coordinates and the corresponding reflections. As a referee, couple occasions I wished that I had access to the data, but my concerns were resolved after the authors provided the omit and difference maps contoured as I requested. I didn't request for the model and data because I felt that I had no right to demand the authors to trust me that I wasn't their competitor trying to solve the same structures, or know someone who does. If I put myself into the authors' position, I would feel uneasy sending my unpublished model and data to an anonymous person. I also felt that as a referee, it wasn't my job to analyze data from which the reported results derived. In the examples that BR mentioned, I wonder if the erronous modeling of the ligands would have been uncovered had the reviewers asked for a simple omit map? >> >> Cheers, >> Quyen >> >> Sent from my BlackBerry 10 smartphone. >> From: Jrh >> Sent: Saturday, January 23, 2016 2:00 AM >> To: [log in to unmask] >> Reply To: Jrh >> Subject: Re: [ccp4bb] questionable structures >> >> Dear James, Dear Colleagues, >> There is one more thing we can all do, namely when asked to referee articles with crystal structures, ask the journal to provide access to the authors' diffraction data and coordinates that are the bedrock of the words of the article. >> >> Recently I learnt that there is 'Peer reviewers openness initiative' described here :- >> http://rsos.royalsocietypublishing.org/content/3/1/150547 >> This article and PRO initiative has a broad coverage and our field is very good in the respects that we have our crystal structure databases with very good user access. Our usual practices during refereeing are not as good as they could be; in my experience i have to ask the journal editor for the diffraction data and coordinates. Having done so the editor and authors have, except in one case, responded promptly with these. Maybe even glad of the keen interest! >> >> The concern you would have perhaps of not having time to repeat the analyses of the authors is dealt with in the article I cite above; see section 'Reviewers concerns'. >> >> Yours sincerely, >> John >> >> On 22 Jan 2016, at 22:18, James Woo <[log in to unmask]> wrote: >> >>> What a ¡®lively debate¡¯ it is! As Herman said, the author should do something to their ¡®bias interpretation¡¯ model, retracting it from pdb and correct in their paper. But for the structure-dominated paper, things may not be that simple and easy. Because every other biochemical or genetic data are used by the author to support their model, if the model is fundamentally incorrect, let alone other part of the paper. It is not just the artificial water or ligand there, but it is the author¡¯s attitude towards to the science. At this point, I fully understand the feeling of BR. >>> >>> There is one question about the oligomeric states of small molecules, like c-di-gmp, c-di-amp, or cGAMP (CDNs). 1, If these molecules are dimer or oligomer in their crystals, does this mean they are prone to adopt dimer or oligomer in solution? 2, If one enzyme or receptor can degrade or bind monomeric CDNs only, does oligomeric state of these small molecules in solution affect their activity (degrading or binding ) dramatically? Thank you in advance! >>> >>> >>> On 22 January 2016 at 04:35, Bernhard Rupp (Hofkristallrat a.D.) <[log in to unmask]> wrote: >>> > ¡°The consensus of these experts is clear that the quality of the data and the level of noise within the electron density map in the Salunke study preclude tracing peptide residues within the x-ray crystal structures.¡± >>> >>> > Isn¡¯t this equivalent to what you suggest, albeit in more diplomatic language? >>> >>> Hmm¡.which part of ¡®and it should not be in any data base¡¯ was unclear? -> cf. continuation Herman >>> >>> >Also, I think your language of ¡°wrong¡± is imprecise (and therefore wrong), as Adrian pointed out. >>> >>> You are correct. The statement is *imprecise* but pretty darn *accurate* ;-) >>> >>> BR >>> >>> >>> >>> >>> >>> From: Bernhard Rupp [mailto:[log in to unmask]] >>> Sent: Thursday, January 21, 2016 2:56 PM >>> To: Keller, Jacob >>> Cc: [log in to unmask] >>> Subject: Re: [ccp4bb] questionable structures >>> >>> >>> >>> Simple statement: "The structure model is is almost certainly wrong (to the point of 'beyond reasonable doubt') and it should not be in any data base." >>> >>> How to handle the rest of the paper depends on the degree of inference based on the flawed model. But I am not doing all the work for the editors ;-) >>> >>> >>> >>> BR >>> >>> >>> >>> On Thu, Jan 21, 2016 at 8:40 PM, Keller, Jacob <[log in to unmask]> wrote: >>> >>> BR: >>> >>> >>> >>> Not clear what more you would have wanted to the editor to write¡ªwhat¡¯s missing? >>> >>> >>> >>> Or were you commenting on the lack of concrete actions? >>> >>> >>> >>> JPK >>> >>> >>> >>> >>> >>> >>> -- >>> >>> ----------------------------------------------------------------- >>> Bernhard Rupp (Hofkristallrat a. D) >>> 001 (925) 209-7429 >>> +43 (676) 571-0536 >>> [log in to unmask] >>> [log in to unmask] >>> http://www.ruppweb.org/ >>> ----------------------------------------------------------------- >>> The hard part about playing chicken >>> is to know when to flinch >>> ----------------------------------------------------------------- >>> >>> >>