Neutron crystallography can be used to gain insight into hydrogen positions. This is extremely beneficial when trying to determine a mechanism. This was the case for endothiapepsin. If one is able to substitute hydrogen for deuterium, the scattering is significantly increased (see slide 14 of Roger Pynn’s presentation on Neutron Crystallography Theory). Deuterons scatter neutrons in a manner similar to that of carbon. In X-ray crystallography, however, we see that they are quite different.
Two methods are used to exchange hydrogens:
1) The crystal can be soaked in deuterated buffer or by placing deuterated water at the ends of the capillary to allow for vapor exchange.
2) The protein can be expressed by using perdueterated media, in which the carbon source for E. coli contains deuterium. Check with your favorite neutron beam line to find out if they offer perdeuteration services. Perdeuteration is the ideal method because nearly all hydrogens can be exchanged. The only downside here is that you may not be able to use the exact same crystallization conditions as the native protein.
If you are considering using neutron crystallography, I would suggest using these two general criteria based on previous published neutron structures.
1) Crystal size ~1 mm^3 or larger
2) Crystal has been solved to ~1 A or better with X-rays
Recently, a nice summary figure and table have been published. They show the current parameters of neutron structures that have been published up to 2007.
Data collection time can be greatly reduced if your crystal is in a high symmetry. High symmetry is a significant benefit in neutron crystallography since it may take 12 hours to collect a frame (mileage will vary depending on beam line).
Finally, it has been proposed that Oak Ridge be able to reduce crystal size to 0.1 mm^3 (pdf). If this is made possible, we may see neutron crystallography becoming a more routine crystallographic technique.
BRENDA is a gold mine for those studying enzymes! The database proclaims to be the comprehensive enzyme information system and with 5010 enzymes it looks to be the case. Here is a screenshot of the navigation bar. As you can see BRENDA brings together many different categories such as IC50 values, pH stability range and crystallization.
My only suggestion so far is to change ‘Recommended Name’ to ‘Enzyme name’. I think it would save some confusion in the search entry.
I have never seen another database bring together this much information about a class of proteins. If you have a colleague working in enzymology this is site is definitely worth passing along.
The way in which scientific publications appear online is going to become increasingly important. How literacy research is conducted is changing rapidly. People are turning to online resources rather than utilizing libraries. Publications that haven’t been made available on the internet may be overlooked. This could result in your paper not being referenced as often, or worse, your research may be repeated.
The number of citations a paper receives helps to determine the impact of the research within that paper. Even if your research is excellent, if no one finds the paper it won’t be cited.
The probability of your paper being read increases the closer it is to the number one search result.
So how do you become the #1 publication in search results?
SEO (search engine optimization) is a field that studies how search engines are influenced by content. The basis for this work is that it is believed that search engines are not perfectly efficient. Therefore with a little tweaking, you may be able to give your publication the boost it needs to be noticed and deemed an appropriate match by search engines. Just to be clear, papers should not be poorly written in an attempt to gain search ranking and in the end content will have a much great impact than SEO.
There are many factors a search engine considers when assembling a results page. The scientist in me cringes a bit at presenting this information since the search algorithms are kept secret making it very difficult to know exactly how search results can be influenced.
Today, we are going to focus on the two items that you can control.
1) Paper Title
2) Keyword Density
Paper Title:
The basics of SEO of titles is that your keywords (the search terms that you people may use to find your paper) should be contained within your title. Although opinions are mixed it is also thought that keywords placed near the beginning have a higher influence than those at the end.
Here’s a great example of how a title should be written for SEO from Acta D:
‘Eukaryotic expression: developments for structural proteomics’
An example of a disadvantageous title would be:
‘The 1.6 Å resolution crystal structure of a mutant plastocyanin bearing a 21-25 engineered disulfide bridge’
The problem here is the resolution of the structure is listed first in the title. More than likely, this paper is going to rank higher for the term ‘1.6 Å’ rather than, for example, ‘mutant plastocyanin’.
If you were the author of this paper and thought each word in that title was critical, it would be more beneficial to arrange the words as follows:
‘Mutant plastocyanin a 1.6 Angstrom crystal structure bearing a 21-25 engineered disulfide bridge’
This tweaked title would be ideal if you were looking to rank for ‘mutant plastocyanin’.
Keywords:
Of course, your paper should be written for humans, but it may help to keep search engines in mind. Although not as influential as in the past increasing the keyword percentage in your document should also help. For example, if you wanted to keyword for ‘protein crystallization’ think about if you can increase the number of times the term is being used.
Again, I don’t have direct proof of how much influence these changes make, but many top brands have excellent top keyword density (percent that term is used on their site) and my feeling is that it wasn’t by accident:
Zappos: shoe (8.33%), shoes (7.78%), zappos (5.00%)
Visa: visa (25.00%), card (10.61%), cards (4.55%), credit (3.03%)
JCrew: crew (6.77%), clothing (3.59%), dresses (3.19%)
Take some time and really think about the title of your paper and what keywords are important. You may find that the one thing standing between you and the first page of Google scholar……is a little tweaking.
P212121 has been more successful than I would have ever imagined. My primary goal has been to help someone in the field of macromolecular crystallography. I hoped that by bring together resources, creating tutorials and answering questions that this website would be helpful.
I also need to say thank you. I have had many readers contribute so much time and effort answering my questions and sharing their experiences. My friends that have share with me more than I given with a comment here, thank you.
If you like numbers, the current RSS count here considering only Google is at 140 as a (probably bad) reference point Acta Crystallographica Section D is at 93.
The blogging community has been wonderful and for fear of leaving someone off of a list, I hope a general thanks will suffice.
This site was also recently included in the science Alltop, which is cool resource for finding science information.
What’s next? I have a lot in the pipeline, but before we get there I would love to hear from you. Have an idea or suggestion to make this site better? If we have spent the last couple of months together and haven’t met just a Hi or Happy Birthday would be great.
Carbohydrates (glycans) are a major class of biological macromolecules along with proteins and DNA molecules. The array of possible combination of carbohydrates is astounding. Here is an extensive list of carbohydrate databases that offer a number of different searching methods as well as entries, enjoy.
1) GlycomeDB is a carbohydrate structure metadatabase that has combined all free databases (CFG, KEGG (right panel), GLYCOSCIENCES.de (no $), BCSDB, GlycoBase (Dublin, Lille) and Carbbank) including both their structures and annotations.
3) O-GlycBase contains 242 glycoprotein entries of both O- and C-glycosylated proteins.
4) Glycan Binding Proteins seems heavily dependent on knowing the CFG ID of your glycan of interest.
5) GLYCO3D breaks down glycans into seperate databases such as monosaccharides, di, oligo, poly, lectins, glycosyltranserases and Gag binding proteins. The search is organized by a series of drop down menus, which is really helpful if you are taking a top down approach (animal to glycan). On the downside, the website has not been updated since May of 2007.
6) Lectins contains lectins from plant, algae, virus, animal, bacteria, yeast and fungus.
7) Carbohydrate-Active enZYmes Database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
Glyco Enzymes is good if you have a monosaccharide and want to find out the glyco-enzymes involved. This database is not for finding structural information such as what is found in the PDB.
At the beginning of the year, we discussed whether the CCP4bb should become a forum. Initially, BioKlatch.com was created by Matt Harrington – the site is now being redirected to MajorGroove.org.
The site is based on StackExchange, which is a new website designed around a simple question and answer format. It will be interesting to see if the pricing changes once the site is out of beta. The site includes a number of community features. On example: the ability to earn badges by performing various activities, from filling out your profile to posing a good question.
The discussions are still kept on the CCP4bb, but the answers/responses are then posted on MajorGroove.org. If the system works well, it should provide an extensive selection of Q&A that have previously been addressed on the CCP4bb.
Are you excited about this new resource? Is this just one more place to visit? I have joined, will you?
For structural information concerning metals and RNA then you may find MeRNA quite helpful (pdf ref). Metals have been shown to play an important role in RNA folding. The MeRNA database currently contains 398 PDB entries which include 22 different metals.
Note: The MESPEUS database is excellent resource for metals and proteins.
The simple periodic table display works well. The results page would be easier to read if the titles were not all in italics.
The advance search offers a number of function with my favorite being the ability to search through 8 different binding motifs. The advanced search also allows for search by reference and/or author.
Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography) has been developed for the determination of macromolecular crystallographic structures. Phenix is a leader in automating the structure determination process.
I am going to start playing around with Phenix, but first wanted bring together helpful resources about the program suite:
In crystallography, updating software and general system maintenance can be quite time consuming. The Structural Biology Grid (SBGrid) was developed to help combat that issue. The SBGrid is currently comprised of 131 laboratories throughout the world. The SBGRid maintains a complete installation of structural biology applications complied and optimized to run on OS X (PPC and Intel), Linux and SGI. SBGrid has an extensive list of crystallographic software.
To become a member you need to contact them for details.
This program could be a real benefit to crystallographers that do not have a background in system administration. Unfortunately, the requirements of joining are not described on their website so am not going to get too excited.
If you are an affiliate of SBGrid, I would love to hear about your experiences.
What do you think about SBGrid? Could this type of program benefit your lab? Do you think this type of setup maybe the future for most crystallography labs?
This is a follow up to the post Is the Beam Center Correct? which shows how to determine if your beam center is correct. Today, we will be looking at how correct the beam center if it is wrong.
The computer screen is not as clear as I would like, but think you will be able to follow along (watching the video full screen should help). The audio is a little hard to hear at the end since I am speaking directly behind the camera. Anyway, I would love to hear your thoughts.
Here is the post on the format of a comm file. We also had a post on the overview of using ipmosflm, which should help you follow along with this post if you get stuck. When I bring up ‘previous set’ am referring to the offset seen in the Is the Beam Center Correct? video.
I would love to hear some feedback on this! Can you follow along? Do you like having videos? I would also love hear suggestions on screen recording software (linux or windows).
would be great.
