home

Archive for the 'namd/vmd' Category

Gumming Up Appetite to Treat Obesity – Vitamin B12 Bioconjugate Project (& Graphic) Mention In Scientific American

Sunday, December 11th, 2011

From the “free press” division of the blog, a recent post by Ferris Jabr on the scientificamerican.com site highlights yet another evolutionarily fascinating application of cyanocobalamin (herein referred to as B12) out of the Rob Doyle Lab for the non-invasive delivery of small molecules into the human-person. Here, a mechanism for the delivery of human peptide YY (hPYY) into the bloodstream via a food-free mechanism (unless you count the gum flavorings as a fruit). From the thorough and accessible article (with a decent balance of sciam and non-sciam redirecting)…

CHEMICAL COUPLE: The appetite-suppressing hormone hPYY hitches a ride with vitamin B-12 from the stomach to the bloodstream (caption credit: sciam).

Losing weight is not always about anticipating swimsuit season or squeezing into skinny jeans—for the clinically obese, losing weight is about fighting serious illness and reclaiming health. But the primal part of the brain that regulates appetite will not place a moratorium on hunger just because someone and their doctor acknowledge the need to lose weight. Researchers at Syracuse University are working toward a unique solution: a stick of chewing gum that suppresses appetite.

A slightly-larger version of the image on the site is reproduced above (with the image credit most welcome on the site). For a bit more information about the general properties of B12 and its potential applications for other diet-related issues, a few articles described here @swv link to more complete discussions…

* Vitamin B12 In Drug Delivery: Breaking Through The Barriers To A B12 Bioconjugate Pharmaceutical

* The Binding Of Vitamin B12 To Transcobalamin(II); Structural Considerations For Bioconjugate Design – A Molecular Dynamics Study

* B12-Insulin Bioconjugate/Transcobalamin(II)/Insulin Receptor Cover Image For The April Issue Of Clinical Chemistry

* New B12-Insulin-TCII-Insulin Receptor Cover Image For This Month’s ChemMedChem (March 2009)

* Exploring the Implications of Vitamin B12 Conjugation to Insulin on Insulin Receptor Binding and Cellular Uptake

B12-Insulin Bioconjugate/Transcobalamin(II)/Insulin Receptor Cover Image For The April Issue Of Clinical Chemistry

Sunday, April 11th, 2010

A brief post about some free research press (and the new addition to the Cover Gallery). Having already been featured on the cover of the ChemMedChem March 2009 issue (see the New B12-Insulin-TCII-Insulin Receptor Cover Image For This Month’s ChemMedChem (March 2009) post) , the side-on view of the B12-Insulin/TCII/Insulin Receptor structure was chosen for this month’s cover of Clinical Chemistry. While the originating article itself is not included in the issue (I should have recommended citing the ChemMedChem article in the image caption), several diabetes-related articles are featured in this month’s issue.

ON THE COVER: Scientists are investigating ways to develop effective oral insulin therapies. One such model is a vitamin B12–insulin conjugate bound to transcobalamin II and is shown here docked in the insulin receptor. The discovery of easier ways to deliver insulin into the blood stream would improve the lives of the millions of individuals living with diabetes. This month’s issue of Clinical Chemistry contains 4 articles related to diabetes. The first 2 articles provide readers with a point/counterpoint discussion of the value of reporting estimated glucose along with Hb A1c. Next is an article on the association of apolipoprotein B with incident type 2 diabetes. Lastly, the development of the first radioimmunoassay for insulin led to a Nobel Prize and is chronicled in this month’s Citation Classic feature. (See pages 545, 547, 666, and 671.) Image reproduced with permission from Damian G. Allis and Robert P. Doyle, Department of Chemistry, Syracuse University.

As a brief explanation of the image, this “scene” is meant to show (without proper molecular dynamics simulations to show how well it would work) that the Transcobalamin(II) transport/protection protein for cobalamin/cyanocobalamin (vitamin B12) and the B12-insulin bioconjugate discussed in the ChemMedChem article is small enough to fit within the Insulin Receptor protein such that insulin may still be able to bind to its receptor. This is the final piece of the puzzle in the proposed mechanism (and experimentally demonstrated event) by which the B12-insulin bioconjugate retains all of the benefits of free B12 (transport from the digestive system to the bloodstream) and insulin (proper receptor binding and the subsequent induction of cellular glucose uptake).

The figure caption and April 2010 Table of Contents can be found in PDF format at the Clinical Chemistry website (with a local copy of the PDF also available HERE.

www.somewhereville.com/?page_id=985
www3.interscience.wiley.com/journal/122250806/issue
www.somewhereville.com/?p=511
www.clinchem.org
en.wikipedia.org/wiki/Diabetes
en.wikipedia.org/wiki/Molecular_dynamics
en.wikipedia.org/wiki/Cyanocobalamin
en.wikipedia.org/wiki/Vitamin_B12
en.wikipedia.org/wiki/Bioconjugate
en.wikipedia.org/wiki/Insulin_receptor
www.clinchem.org/content/vol56/issue4/

New B12-Insulin-TCII-Insulin Receptor Cover Image For This Month’s ChemMedChem (March 2009)

Sunday, March 15th, 2009

As was the case for the first ChemMedChem December, 2007 cover issue (posted previously), the cover story in this month’s issue is a communication by myself and members and collaborators of the Robert Doyle Group here at Syracuse University.  In this case, the work for the cover image actually went into computational research published in the associated article (instead of just a pretty cover image to complement the associated article, which was the intent of the previous cover).

The image below shows the Transcobalamin II (TCII) protein (in teal ribbons, with a bound cyanocobalamin (B12) shown in red.  The PDB code for this complex is 2BB5) sitting within the surface-accessible fragment of the gigantic insulin receptor (PDB code 2DTG.  The cell membrane would be at the bottom of this image, with the remainder of the complete protein sitting both within the cell membrane and then into the cytoplasm).  Saving the lead-up to this structure generation for the associated published article, this image was created to show one of the most important steps in the Oral Insulin project being worked on in the Doyle Group, with the fact that we know it works making the validity of the image content all the more relevant.  In brief, this figure shows that the TCII/B12-Insulin complex can fit within the insulin receptor such that the insulin molecule can bind to its receptor position on the appropriately described insulin receptor (IR), thereby instigating the cascade of events that leads to cellular glucose uptake.

For a larger view, click on the image.

Like many of the protein structures I render, this image would not have been possible without VMD and MegaPOV, my favorite OSX POV-Ray variant (there’s quite a bit of Photoshop layering as well).  The final layout for the cover is below, which I think would have benefited from the aerial view on the upper left side being shifted slightly to the left to fill out the black square.

According to the ChemMedChem website:

The cover picture shows three views of a vitamin B12-insulin conjugate bound to transcobalamin II, docked in the insulin receptor (IR). This study reveals how the structure of an orally deliverable insulin changes in solution after vitamin B12 conjugation and its effect on IR binding capacity. The results demonstrate that chemical modification of insulin by linking relatively large pendant groups does not interfere with IR recognition. For more details, see the Full Paper by T. J. Fairchild, R. P. Doyle, et al. on p. 421 ff.

To date, the associated work has received some additional linkage, both in the form of inclusion in the Spotlight list in Angew. Chem. Int. Ed. 2009, 48, 2072 – 2073 and, for those looking for a more pop-sci discussion of the applications of the research, New Scientist (Insulin Chewing Gum, 14 January 2009).  PDFs of the associated content are provided here for Angewandte Chemie and New Scientist.

There is a considerable amount of additional computational work being done on this system and the complete B12 pathway for potential use in various other applications.  Stay tuned for next year’s cover.

www3.interscience.wiley.com/journal/110485305/home
www3.interscience.wiley.com/journal/117354609/issue
www.somewhereville.com/?p=103
chemistry.syr.edu/faculty/doyle.html
www.syr.edu
en.wikipedia.org/wiki/Transcobalamin
en.wikipedia.org/wiki/Cyanocobalamin
www.rcsb.org/pdb/home/home.do
www.rcsb.org/pdb/explore/explore.do?structureId=2BB5
en.wikipedia.org/wiki/Insulin_receptor
www.rcsb.org/pdb/explore/explore.do?structureId=2DTG
en.wikipedia.org/wiki/Cytoplasm
en.wikipedia.org/wiki/Insulin
www.ks.uiuc.edu/Research/vmd
megapov.inetart.net
www.apple.com/macosx
www.povray.org
en.wikipedia.org/wiki/Adobe_Photoshop
www3.interscience.wiley.com/journal/122232189/issue
www.newscientist.com/article/dn16413-invention-insulin-chewing-gum.html

Exploring the Implications of Vitamin B12 Conjugation to Insulin on Insulin Receptor Binding and Cellular Uptake

Friday, November 21st, 2008

In press, in the journal ChemMedChem (and, because I think it’s hip, I note that the current “obligatory” image for the wikipedia article for ChemMedChem features the image I made for the review article on the topic addressed in this new study). As with many theory papers (there’s some experiment in there, too), this very brief article summarizes several months of cyanocobalamin (B12) parameterization and molecular dynamics (MD) simulations. The purpose of the theory was to address all of the major structural snapshots in the uptake process associated with the insulin-B12 bioconjugate being developed as part of the much heralded oral insulin project in Robert Doyle’s group here at Syracuse. These structures include:

1. The structure and dynamic properties of the insulin-B12 bioconjugate
2. The binding of B12 to Transcobalamin II (TCII) (for B12 parameterization)
3. The binding of the insulin-B12 bioconjugate to TCII (and the steric demands therein)
4. The interaction of the insulin-B12 bioconjugate, bound to TCII, with the insulin Receptor (IR)

The quantum chemical (for the B12 geometry and missing force constants) and molecular dynamics (GROMACS with the GROMOS96 (53a6)) simulation work is going to serve as the basis for several posts here (eventually) about parameterization, topology generation, and force field development.

As an example of some of the insights modeling provides, the figure above shows the insulin-B12 bioconjugate (the insulin is divided into A and B chains, the A chain in blue and the important division of the insulin B chain in the front half of the rainbow). Insulin is a rather large-scale example of many of the same molecular issues that arise in the analysis of solid-state molecular crystals by either terahertz or inelastic neutron scattering spectroscopy. The packing of molecules in their crystal lattices can lead to significant changes in molecular geometry, be these changes in the stabilization of higher-energy molecular conformations or even deformations in the covalent framework. In the case of insulin, it is found that the crystal geometry (also the geometry of stored insulin in the body) is quite different from the solution-phase form. It’s even worse! The B chain end (B20-B30) in the solid-state geometry covers (protects?) the business-end of the insulin binding region to the Insulin Receptor. One can imagine the difficulty in proposing the original binding model for insulin to its receptor from the original crystal data given that the actual binding region is blocked off in the solid-state form! The “Extended” form in the figure is representative of “multiple other” conformations of the B20-B30 region (which mimics the characterized T-state of insulin), those geometries for which the insulin binding region (blue and green) is completely exposed. This extended geometry is also the one that separates the bulk of the insulin structure from the covalently-linked B12 (at Lys29) and, it is argued from the MD simulations in the paper, enables the B12 to still tightly bind to TCII despite the presence of all this steric bulk.

Amanda K. Petrus1, Damian G. Allis1, Robert P. Smith2, Timothy J. Fairchild3 and Robert P. Doyle1

1. Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
2. Department of Construction Management and Wood Products Engineering, SUNY, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
3. Department of Exercise Science, Syracuse University, Syracuse, NY 13244, USA

Extract: We recently reported a vitamin B12 (B12) based insulin conjugate that produced significantly decreased blood glucose levels in diabetic STZ-rat models. The results of this study posed a fundamental question, namely what implications does B12 conjugation have on insulin’s interaction with its receptor? To explore this question we used a combination of molecular dynamics (MD) simulations and immuno-electron microscopy (IEM).

www3.interscience.wiley.com/journal/110485305/home
en.wikipedia.org
en.wikipedia.org/wiki/Chemmedchem
www3.interscience.wiley.com/journal/116323633/abstract
en.wikipedia.org/wiki/Cyanocobalamin
en.wikipedia.org/wiki/Molecular_dynamics
en.wikipedia.org/wiki/Insulin
chemistry.syr.edu/faculty/doyle.html
chemistry.syr.edu/faculty/doyle_group/index.html
www.syr.edu
en.wikipedia.org/wiki/Quantum_chemistry
www.gromacs.org
en.wikipedia.org/wiki/Terahertz
en.wikipedia.org/wiki/Inelastic_neutron_scattering
chemistry.syr.edu
www.syr.edu
www.esf.edu

Oral Insulin Delivery Cover Image (And Associated Syracuse Research Article) in ChemMedChem

Tuesday, December 4th, 2007

You’ve heard about it, you’ve read about it, you’ve seen it on color TV, you’ve even seen it streamed. The cover story in this month’s issue of ChemMedChem is a communication by members and collaborators of the Robert Doyle Group here at Syracuse University. The report describes the B12/TCII-based uptake of insulin, a process that occurs via the ingestion of a B12-insulin conjugate. In case you missed that, the delivery is oral, not by needle. For those of us that pass out at anything needle-related at about the time that the alcohol wipe is opened, that’s a positive step forward for getting rid of any syringe-related medicine altogether.

full image

With the cover story comes the cover image shown above, a structure calculation on the insulin-B12/TCII complex. The bases for this structure can be found in the Protein Data Bank, including the TCII-B12 complex reported in PDB entry 2BB5 (the only hack in the structure calculation involved the replacement of the cobalt for iron to use already available bond parameters) and the insulin structure reported in PDB entry 1ZNI. The covalent attachment of the insulin to B12 can be found in the article. Structure manipulation was performed with a combination of NanoEngineer-1 and VMD, VMD being included in the mix in order to generate the ribbon renderings of the insulin and TCII protein backbones. As for the accuracy of the calculation, time and a synchrotron X-ray source will tell.

For much more information and numerous links to new stories related to the research in the article, I direct you to the group website of Robert Doyle and the various links to news stories available in his departmental publication list.

chemmedchem cover
From ChemMedChem. Click HERE to go to the article.

From the website:

Cover Picture: Vitamin B12 as a Carrier for the Oral Delivery of Insulin (ChemMedChem 12/2007). The cover picture shows an orally active, glucose-lowering vitamin B12-insulin conjugate bound to the B12 uptake protein transcobalamin II (TCII). The inset shows a close-up view of the TCII binding pocket. (Insulin is in red; vitamin B12 is in bright yellow.) For details, see the Communication by T. J. Fairchild, R. P. Doyle, et al. on p. 1717 ff.

www3.interscience.wiley.com/journal/110485305/home
chemistry.syr.edu/faculty/doyle.html
www.syr.edu
www3.interscience.wiley.com/cgi-bin/abstract/117354616/ABSTRACT?CRETRY=1&SRETRY=0
en.wikipedia.org/wiki/B12
en.wikipedia.org/wiki/Insulin
en.wikipedia.org/wiki/Transcobalamin
www3.interscience.wiley.com/journal/117354609/graphissue
www.rcsb.org/pdb
www.rcsb.org/pdb/explore.do?structureId=2BB5
www.rcsb.org/pdb/explore.do?structureId=1ZNI
www.nanorex.com
www.ks.uiuc.edu/Research/vmd
en.wikipedia.org/wiki/Synchrotron
chemistry.syr.edu/faculty/doyle_group/index.html
chemistry.syr.edu/faculty/doyle.html#pubs

Obligatory

  • CNYO

  • Sol. Sys. Amb.

  • Ubuntu 4 Nano

  • NMT Review

  • N-Fact. Collab.

  • Pres. Asn. CNY

  • T R P Nanosys

  • Nano Gallery

  • nano gallery
  • Aerial Photos

    More @ flickr.com

    Syracuse Scenes

    More @ flickr.com