About the Author - Peter Nollert

Peter Nollert

I'm Peter Nollert and I write this blog to point researchers to topics that are relevant to protein crystallization. My mission is to help spread knowledge that is 'out there on the web' and help you succeed with your protein structure research.  I oversee the membrane protein research and technology development activities at Emerald BioStructures. Check out The GPCR blog, or my publications

Blog Archive

Protein Crystallization Hits

The protein-crowded cytoplasm: a Work of Art

by Peter Nollert
March 27, 2013 20:40

Many X-ray crystallographers have told me that images of protein structure have contributed in their decision to become structural biologists. For me, it was a David Goodsells 1992 book "The Machinery of Life"  that showed protein structures in the cellular context (here's some of Goodsell's current work). Such images give a tangible impression that the inner workings of cells and show that protein molecules are akin to engineered machines with precisely developed mechanics. 

I was happy to see that there are scientists/artists following this tradition of creating such fascinating imagery.  But rather than drawing cartoons of protein particles (based on experimentally derived structures, mind you) Sean R. McGuffee and Adrian Elcock  have set up brownian dynamics simulations of a cytoplasm consisting of 50 proteins and, and this is the crucial control, reproduce experimental parameters.

 

This is a snapshot of their model of macromolecules in the cytoplasm:

 

As real as it gets in a computer: a fascinating image of a computational simulation of macromolecules in the cytoplasm. Taken from: http://www.flickr.com/photos/dullhunk/4464549449/sizes/o/in/photostream/

 

 

McGuffee, S. R. and A. H. Elcock 

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

PLoS Computational Biology 6 (3), e1000694+ (2010)

dx.doi.org/10.1371/journal.pcbi.1000694

 

Enjoy,

Peter

Tags: Computer | Opinion

Full transparency for all protein crystallization formulations from Emerald Bio: of course!

by Peter Nollert
May 15, 2012 01:40

If I buy a reagent kit for my research, I need to know what's inside. Of course, how else can you carry out an experiment? I can not agree more with Anna Git's complaints in an Nature Comment that there is a lack of transparency imposed by some reagent manufacturers. (see Git, A. (2012). Research tools: A recipe for disaster Nature, 484 (7395), 439-440 DOI: 10.1038/484439a). Here are her grievances:

'For the most part, [reagent manufacturers] do not provide full details about the contents of their chemicals,…'
'...to try to decipher the ingredients of commercial products, my colleagues and I have tested pH and conductivity, signed confidentiality agreements to receive extra information not on the label and discarded experiments in which unknown ingredients impeded subsequent reactions. We are on first-name terms with many sympathetic scientists who work in research and development (R&D) for commercial vendors, and who occasionally whisper crucial details off the record.'

So here's our stance on this subject: Emerald Bio customers can get all recipe data that goes into any of our reagent kits. Most of this data is supplied in the various tech sheets. For instance, see here for a description of the 96 Wizard III/IV protein crystallization formulations. Should this information not be sufficient for you, call us toll free at 1-888-780-8588 and ask us what else you need. We're glad to share with you more detail on any of our protein crystallization formulations. For instance, recipes for formulations in any of our protein crystallization screens, down to the CAS number if you need, and even raw material supplier information. No need to whisper or sign any confidentiality agreements. 

Why are we doing this? Service to our customers who trust us as a no-formulation secrets manufacturer. And in the long run this openness is in our own interest: Your success in reproducible protein crystallization is our business. 

Thank you for your continued use of our products,

Peter

Tags: Announcements | Best practice | Opinion

Best of 2010 in Protein Crystallography

by Peter Nollert
December 7, 2010 01:42

This is the list of answers that I got today from a quick and informal survey that I conducted over 'lunch' with some of our crystallographers: 'what's been the best thing that happened in 2010 in the world of crystallization / crystallography?'

Here we go with the highly opinionated 'Best of 2010 in Protein Crystallography' (in no particular order):

These are my two personal favorites in the 'Best New Software' category: Mendeley (keeping track of ones research PDF collection) and new de-novo feature of the E-Wizard online crystallization screen generator. But where's the 'best 2010 protein crystallization iPhone app?'.

Not directly related to the field of protein crystallography, but this one could serve as an example for us crystallographers:

  • The clever choice of the name for the bacteria that have phosphate exchanged by arsenate atoms. Strain GFAJ-1 stands for "Give Felisa A Job" (first author of the paper is Felisa Wolfe-Simon).

Happy 'last days of the decade without a name',

Peter

Tags: Awards | Crystalization Tips | Job market | Literature | New Techniques | Online Tools | Opinion | Phasing

7 Ways to Maximize the Value of your Protein Crystallization Paper

by Peter Nollert
November 2, 2010 22:22

For an academic researcher paper writing is often the culmination of hundreds, if not many thousands of hours of work. The data is collected, a story is shaping up - how do you go about transmitting your newly found wisdom to your peers?

I have witnessed firsthand several different paper writing styles and practices and am the first to admit that there's no single best way to this. There's some good advice out there, though. For example, Bill Wells suggests in his aptly titled paper "Me Write Pretty One Day: How to Write a Good Scientific Paper"  'a few small steps" to make "...scientific writing clear, straightforward, and digestible". As I'm starting to write a paper myself I find it useful to look at this paper to remind myself of how to write clearly, to define what's my point and then adhere to the 'show, don't tell' rule. Wells guides his readers through 'The Anatomy of a Paper' and gives a lot of good advise on how to tell our story.

As a reader of a protein crystallization paper I expect to see the following:

1. The amino acid sequence of the protein that's expressed.

2. Description of a typical expression and purification experiment. What's the yield & purity? Are there functional assays that provide checkpoints for anybody who wishes to repeat your work?

3. A detailed description of what happened between eluting the protein from the last column and before setting it up for crystallization: temperature(s), storage conditions and time, dialysis (time, volume, MWCO used, volume ratio), concentrating device, centrifugation, filtration, addition of ligands.

4. The crystallization experiment/regime: composition of precipitant solution buffers, crystallization type, volumes, trays, dispensing methodology (stirred or mixed?), screen used, time it took for crystals to show up. Any 'out of the norm' observations, such as 'crystals formed at the air liquid interface'

5. Crystallization result: how many crystals, crystal habit, size, crystal quality (X-ray diffraction limit and any 'Table 1' associated data that resulted from a complete data set). Describe reproducibility (only 1 drop out of 10 produced crystals?, only 1 out of 10 crystals diffracted?) and any insight gained while handling the crystals (did the crystals bend when looping out, do they tend to break? Do they 'melt' when the temperature is changed?).

6. X-ray diffraction experiment: treatment of crystal (cryo used, orientation crystal was mounted) before and during exposure to X-rays. Diffraction equipment used, exposure time, sweep angle.

7. Two images of the crystals: close-up to see the crystal habit and an overview of the entire crystallization experiment. An X-ray image showing diffraction spots (crystal oriented along a special axis would rock).

There's really no good reason to hold back with any such details in a protein crystallization paper (I won't hold it against you when I review your paper). After all, one of the reasons you're writing the crystallization paper is that you aim to provide instructions to a crystallizer who seeks to enable repetition of your work in the future. This is a neat way you can 'pay back' to all scientists that provided you with insightful tips in their papers and that have helped you succeed with your own protein crystallization research project. Pass on the baton.

Cheers, Peter

Tags: Best practice | Crystal images | Literature | Opinion

How to keep your protein crystallization papers organized

by Peter Nollert
October 5, 2010 14:08

Over the past two years I've systematically reduced the amount of printed paper in my office as well as in my private life. The idea behind this effort is that 'going digital' with all my documents will make it simpler to store and quickly find information that I need. This is work in progress where the crucial software elements that stuck are Sync Toy (general file housekeeping), PICASA (automatic archiving of images) and Google Desktop (searches everything I have on my PC; yes - I'm a PC).

The most recent addition to this toolset is Mendeley. This is a PDF file organization tool that's devised specifically for researchers to archive, annotate and share their PDF articles. To say the least, I'm very impressed with Mendeley's utility. Within a short period of time Mendeley has helped me to aggregate and organize all of my (currently 642 and growing library of) PDF documents. The functionality goes well beyond a traditional Reference Manager. Features are here, the ones that I like particularly are:

  • making notes within PDFs,
  • sharing libraries over the web,
  • backing up my own collection of articles,
  • cross-talk with Zotero (a Firefox-based reference manager),
  • cross-platform compatibility (I have Mendeley installed on Windows 7 and on iPhone/iPod touch, and use it via the web browser interface - works seamlessly so far) and
  • search functionality.

Here's a quick primer to Mendeley:

Mendeley Teaching Presentation

Mendeley : the best research tool since streak-seeding?

There's even a social media facette too; here's my Mendeley profile - friend me if you'd like: 

Oh - and did I mention that Mendeley is available for free?

Cheers,

Peter

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