Archive by category: Behind the Scenes

Consortium progress and scientific advances discussed at third annual meeting

2013 group photoClick to enlarge.

For the third year in a row, the Membrane Protein Structural Dynamics Consortium (MPSDC) hosted a number of events in its home base of Chicago during the month of May, key among these its third annual meeting. Unlike last year’s Frontiers in Membrane Protein Structural Dynamics conference, this year’s annual meeting was closed to the public, although there are plans to host a second open attendance conference in the near future.

Core workshops and minisymposium

As in previous years, the MPSDC’s Computational Modeling Core hosted a membrane protein modeling workshop, and a mini-symposium concerning the latest advances in computational approaches to the study of membrane proteins. As before, the modeling workshop provided attendants with an overview of the use of the modeling dynamics and visualization software NAMD and VMD, and also featured Dr. Wonpil Im’s CHARMM-GUI Ligand Binder module. This year’s mini-symposium covered a number of topics including force field and atomic models, structural modeling with low-resolution data, and transition pathways. The minisymposium hosted a “keynote” lecture of sorts on 2D-IR Spectroscopy, held by Josh Carr from the University of Wisconson-Madison. We are pleased to present you with a recording of Carr’s lecture, titled Connecting Experiment and Simulation by Modeling the Protein Amide I Band.

This year, the Consortium’s Membrane Protein Expression/Purification Core held its first workshop as well. This workshop featured several Consortium collaborators such as Edith Buchinger from Goethe University, Stephen Pless and Lilie Leisle from the University of Iowa, and Andrzej Rajca from the University of Nebraska. Topics discussed at this workshop included cellular and cell-free production of membrane proteins, reconstitution, incorporation of unnatural amino acids, single antigen binder technologies, and chemistry of protein modification and nitroxide spin labels. Both workshops and minisymposium were well attended and productive, and we will continue to host such satellite events in the future.

Annual meeting

The MPSDC’s annual meeting allows for Consortium PI’s to present on the latest advances in the respective cores and projects, and serves as a dedicated time and space for members to discuss their research and organically find ways to collaborate with colleagues. Moreover, it gives the executive arm of the MPSDC the opportunity to report on “the state of the Consortium.”

At this year’s annual meeting at the University of Chicago’s Gleacher Center, MPSDC director Eduardo Perozo highlighted the continual exchange of ideas within and dynamics of the Consortium itself. Focusing specifically on the activities of the past year’s accomplishments, Dr. Perozo discussed the rational and efficient consolidation of Core Facilities to their highest efficiency and optimal productivity in close collaboration with individual projects. For example, the Computational Modeling core is starting to provide a number of services and home-developed algorithms to the community at large, from quick force field parameterization of small molecules (and potential membrane protein ligands) to the conformational energetics biophysical probes, to important tools to the use and interpretation of long range distances and distance distributions from DEER experiments. Additionally, Dr. Perozo reported on the status of the Consortium’s unique bridging and pilot projects. Four of our bridging projects are currently in full swing, and one of the pilot projects has successfully transitioned to bridging project status. We have also incorporated two exciting new Pilot projects that bring new systems and new techniques to the Consortium.

Followed by Dr. Perozo’s framing discussion, the PI’s of each of the three cores and seven projects described the progress made and latest scientific findings in their respective teams, providing attendees with the opportunity to respond and provide helpful feedback. The cores are designed to act as “innovation incubators” and research support centers by providing service and expertise in these critical areas: Membrane protein expression, the establishment of chemical synthesis capabilities for probes and detergents, the generation of a variety of binders and other crystallization chaperones and other target binders and the development of common computational tools to interpret and integrate the wealth of experimental data. Each of these feed and interconnect with individual projects in a highly interactive way.

The Consortium’s projects are integrated as research efforts that tie together or enhance the contribution of the independent work and expertise of the participating investigator to the Consortium and expand the independent work in new directions. Ten talks in all, each of the PI’s of the MPSDC’s cores and projects presented on the very latest activities, which will soon be disseminated to the public in the form of publications and resources.

On the second day of the annual meeting, we featured presentations from a number of our associate members. Associate members are junior faculty members who are pursuing exciting and innovative research parallel to the Consortium’s mission, and have therefore been given access to the interactions and core resources of the Consortium in a budget-neutral way.

Several of our associate members have gone on to participate full-fledged in the Consortium’s activities, either by way of participating in existing projects (such as Wonpil Im with the Computational Modeling Core or Chris Ahern with the Membrane Protein Expression/Purification Core) or by starting new pilot projects. Both Olga Boudker and Ming Zhou started as associated members, and after presenting on their research at last year’s conference have gone on to spearhead new and promising pilot projects.

Along these lines, we invited several of our associate members to present talks, in order to foster further cross-pollination between our research and theirs. This year, Luis Cuello from Texas Tech University presented on inactiviation gating at the K+ channel selectivity filter, Katherine Henzler-Wildman from Washington University presented on the mechanism of multi drug efflux by EmrE, Jens Meiler from Vanderbilt University presented on membrane protein structure & dynamics from limited experimental data, and Robert Keenan from the University of Chicago gave a talk on tail-anchored membrane protein insertion at the ER. In addition to Andrzej Rajca who participated in the Membrane Protein Production core workshop and other associate members like Francis Valiyaveetil, all of them bring state of the art expertise in different areas such as synthetic chemistry and chemical biology, and are expected to actively participate in several of the Consortium’s activities.

In sum, we are thrilled to report that the Consortium is thriving, from both a strictly scientific stand point as well as in regards to our output to the community. We’d like to thank all who attended and partook in this year’s discussions, and look forward to seeing you next year!

Below are several photos of the annual meeting and satellite events. You can either browse through the photos here or visit the set on Flickr.

First Frontiers in Membrane Protein Structural Dynamics Conference was a success

Dorothee Kern, Brandeis University and External Advisory Committee Member

On May 3rd and 4th, the Membrane Protein Structural Dynamics Consortium (MPSDC) held its first Frontiers in Membrane Protein Structural Dynamics conference. The conference consisted of scientific sessions and poster presentations, and featured both Consortium members and external invitees. Attendance was open to the public took place within the context of our 3rd Annual MPSDC Meeting, where all members, NIH representatives and our External Advisory Committee participated. Prior to the conference, the MPSDC’s Computational Modeling Core hosted a NAMD/VMD workshop and a mini-symposium concerning the latest advances in membrane protein modeling.

Miguel Holmgren, NINDS and collaborator in Bridge 1: Conformational Transitions in P-class ATPases

Both the conference and CMC events were very well attended and enabled extensive conversations surrounding the topic of cutting edge advances and scientific methods in the field of membrane protein dynamics, as well as ways to resolve current roadblocks. The conference was able to hit a high note in bringing together the issues and ideas most relevant to the key goals of the consortium both in the present and in the future. Chris Ahern of the University of British Columbia and MPSDC Associate Member noted afterwards that it was probably one of the best meetings he’s been to, “primarily because of the quality of the science that’s being done, as well as the excitement and eagerness of people to cooperate.”

José Faraldo-Gómez, Max Planck Institute for Biophysics and MPSDC Associate Member

In the afternoon, two discussion panels were held, which themselves are in the spirit of much of the broader conversations that took place at the conference as a whole. The first panel, “Finding a common language: linking experiment and computation” was chaired by Hassane Mchaourab, and included Benoît Roux, Martin Zanni, Ivet Bahar, Dorothee Kern, and Emad Tajkhorshid as participants.

Chris Ahern, University of British Columbia and MPSDC Associate Member

The second panel was titled “Breaking the barriers of membrane protein expression and labeling” and was moderated by Robert Nakamoto. The panel included Chris Ahern, Jim Bowie, Volker Dötsch and Shohei Koide. Discussion focused on three topics: the optimal nitroxide spin probe for monitoring protein dynamics and DEER distance measurements, how to incorporate such a probe into the protein targets, and cell free synthesis of target proteins. The optimal nitroxide spin probe would be connected to the backbone by only a β carbon. Such a label can be introduced using chemical synthesis, but because most of our proteins are too large, methods for bio-incorporation of unnatural amino acid are preferred. Cell free biosynthesis systems such as those developed in the laboratory of Volker Dötsch, Goethe University, and Chris Ahern, University of British Columbia, may provide the best approaches. The Protein Core labs will explore methods for charging the non-sense tRNA by evolved tRNA synthetases or a ribozyme using technologies called the Flexizyme developed by Soga and co-workers at Tokyo University. The acylated TAG tRNA charged with the spin probe is simply added to the cell free synthesis mix. Another issue is the lability of nitoxides to reduction by ascorbic acid. We will test a variety of nitroxide spin probes, which have been reported to be relatively insensitive to reduction. Finally, we discussed specific placement of labels using synthetic binders. In particular, the synthetic 10FN3 binders, or monobodies (~93 aa, derived from a type III fibronectin domain), can mediate specific labeling of a protein and effectively attach a label or cargo to the protein target with high affinity and stability.

We’d like to thank all who attended and partook in the discussions. By all accounts, it is hard to think of a better outcome for the conference and accompanying events, and we look forward to hosting another meeting in two years.

Below is a gallery displaying photos of the conference. You can either scroll through the photos here or visit the set on Flickr. We’ve also made available several brief audio interviews with attendees of the conference, to be found in the margins of the body of this post.

Benoît Roux and the Computational Modeling Core

We are delighted to introduce the latest feature on the Membrane Protein Structural Dynamics Consortium (MPSDC) website: Behind the Scenes. Within this section, we will be exploring the inner workings of the Consortium with a camera in hand, dedicating to showing you what takes place within the laboratory setting and outside of it.

For our inaugural piece, we present the following video feature of Benoît Roux, the PI of the Consortium’s Computational Modeling Core (CMC). We sat down with Benoît and asked him about computational modeling, the CMC’s collaborations and function within the MPSDC, and where he sees the Consortium in five years. Let us know what you think in the comments!

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