2014 | Membrane Protein Structural Dynamics Gateway

Anatrace Poster & Travel Award recipients announced

Posted on May 9, 2014 — No Comments ↓

As previously announced, Anatrace has graciously sponsored travel awards and poster prizes for students and postdocs attending the meeting. Four travel awards ($500) and two poster prizes were decided by a panel on the basis of merit. Winners of these awards were announced at the meeting, and can now be released to the public.

The winners of the Anatrace poster & travel awards are:

Poster Awards:

Anne Georges, Washington University of St. Louis
Investigating the inhibitory effects of a novel monobody on EmrE transport activity

Zachary James, University of Minnesota
EPR Detects Changes in the Transmembrane Region of the SERCA-PLB Complex Upon Ser16 Phosphorylation

Travel Awards:

Adam Chamberlin, University of Calgary
The gating pathway in the voltage-gated proton channel

Michael V. LeVine, Weill Cornell Medical College
NbIT – a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter

Nicholas Woodall, University of California, Los Angeles
The positive-inside rule is a local effect

Emilia Ling Wu, University of Kansas
E. coli Outer Membrane and Interactions with OmpLA

Congratulations to all recipients!

New Webserver: ANMPathway determines the most probable (lowest energy) transition pathway between two stable endpoints of a conformational transition

Posted on May 5, 2014 — 4 Comments ↓

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints.

ANMPathway determines the most probable (lowest energy) transition pathway between two stable endpoints of a conformational transition. Conceptually, ANMPathway represents a direct application of the string method to a two-state CG system approximated by ANM energy surfaces. The result is a sequence of PDB structure (a “string”) smoothly linking the two endpoints.

Goals

Generates a continuous minimum energy pathway from two End-Point PDB structures containing the same number and order of residues.
ANMPathway sends the calculated pathway by email. Typical jobs take several minutes to an hour (maximum 12 hours). The result also contains a movie of the structural transition along the calculated pathway and a list of non-native contacts formed during the transition.
NAMD scripts for converting the CG pathway to an all-atom pathway is coming soon.

Webserver: http://anmpathway.lcrc.anl.gov/anmpathway.cgi/

This webserver was developed by Avisek Das and Sunhwan Jo from Benoit Roux’s group at the University of Chicago. Please contact us with questions or suggestions using the comments form below.

Collaborative LeuT study provides new view of neurotransmitter transporters

Posted on April 25, 2014 — No Comments ↓

Model of LeuT alternating access inferred from the crystal structures.

This week, the Transport Cycle in Neurotransmitter Uptake Systems bridging project of the Membrane Protein Structural Dynamics Consortium (MPSDC) published an important article in Nature Structural & Molecular Biology on the bacterial leucine transporter (LeuT), a transporter which is structurally and functionally similar to neurotransmitter transporter proteins that direct neurotransmitters from synapse and terminal nerve signaling. The publication, titled “Conformational dynamics of ligand-dependent alternating access in LeuT,” was spearheaded by Vanderbilt graduate student Kelli Kazmier and Professor of Molecular Physiciology & Biophysics Hassane Mchaourab, and also featured collaboration by Consortium colleagues Jonathan Javitch, Harel Weinstein, and Benoît Roux.

The Transport Cycle in Neurotransmitter Uptake Systems project explores the conformational changes and dynamic properties relevant to function in Neurotransmitter transporters translocation cycle using a combination of computational, functional, and spectroscopic approaches. Using the recently determined crystal structure of a prokaryotic leucine transporter (LeuT), the scientists collaborating in this project are modeling the transport mechanisms of these proteins.

In this study, Mchaourab and colleagues used spectroscopic tools to make dynamic measurements in LeuT, in order to elucidate sodium- and leucine-dependent conformational This work highlights the importance of assessing the mechanistic identity of crystal structures, demonstrates the importance of dynamics in understanding function and realizes the vision of the consortium in integrating teams of scientists towards defining mechanistic principles of membrane proteins.changes in the transporter. The results identify the structural motifs that underlie the shift of LeuT between its various states – outward-facing, inward-facing and occluded. The conformational changes reported present a dynamic picture of the alternating-access mechanism of LeuT and NSSs that is different from the inferences reached from currently available structural models.

The publication marks a significant advance for the project’s research objectives, and is demonstrative of the cutting-edge collaborations between experimentalists and computationalists within the Consortium. According to Mchaourab, this work “highlights the importance of assessing the mechanistic identity of crystal structures, demonstrates the importance of dynamics in understanding function and realizes the vision of the consortium in integrating teams of scientists towards defining mechanistic principles of membrane proteins.”

The publication was also featured in Research News @ Vanderbilt. Click to read »

New webserver: prediction of LBT (lanthanide-binding tag) insertion onto membrane proteins

Posted on April 24, 2014 — No Comments ↓

Background

In recent years, high-throughput genomic and proteomic projects have been revealing new genetic information at a very fast pace. The proper interpretation of such information in the context of the underlying biological mechanisms generally requires studies on a molecular level through biophysical and biochemical experiments as well as biomolecular modeling. Hence, the use of biophysical probes that can be easily integrated into protein structures for functional and structural characterization is becoming increasingly common. Lanthanide-binding tags (LBTs) are a class of such probes that are optimized for binding lanthanide ions.

We have created a fully automated webserver for the prediction of LBT insertions onto existing protein structures. The underlying method uses a coarse-grained backbone+Cβ representation of the protein and samples on the backbone dihedral angles. The method predicts the proper conformation of the LBT tag with respect to the parent protein in existing fusion crystal structures. On multiple membrane protein systems, the method’s prediction of feasibility of LBT insertion on various sites qualitatively agree with the experimental data. The method currently reports several metrics to assess the quality of LBT insertion in a specific site in a parent protein. We expect the method to serve as a useful computational tool for experimentalists by helping them select reasonable sites in a given parent protein where the LBT insertion will likely be successful.

Goals

Given a parent protein where the LBT tag is to be inserted, the method will predict the likelihood of a successful LBT insertion at a certain site in the parent protein.
Given a parent protein and a site of insertion, the method will predict the proper conformation of the parent+LBT fusion conformation.

Webserver

http://goo.gl/1m0Yib

This webserver was developed by Aashish Adhikari from Tobin Sosnick’s group at the University of Chicago. Please contact us with questions or suggestions using the comments form below.

Announcing the Anatrace Travel and Poster Awards

Posted on April 24, 2014 — No Comments ↓

In collaboration with Anatrace, we are delighted to announce travel and poster awards for student and postdoctoral fellows attending Frontiers in Membrane Protein Structural Dynamics 2014.

Four travel awards ($500) and two poster prizes will be decided on the basis of merit.

Anatrace is a privately owned business which specializes in the production of high-purity detergents, lipids, customs. Well regarded as top performers for membrane protein structural biology, Anatrace products are chosen for their uniquely pure molecules – and the exacting chemistry behind them.

Eligibility: graduate students or post-docs with submitted posters.

How to apply: fill out this form.

Deadline: Friday, May 2nd, 2014.

Announcements about awards will be made during the meeting. If you have any questions, please contact us at memprotein2014@gmail.com.

Note: submitting a poster presentation is mandatory for being considered for this award. Student / participant poster abstracts are due by Friday, May 2nd, 2014. You can submit a poster abstract here.