Conformational states of membrane proteins: Technology development for bioscience

Lead Research Organisation: University of St Andrews
Department Name: Chemistry


Although life requires water, life must be able to control the flow of water. As an example, if a person (70% water) jumps into a swimming pool they do not dissolve like a sugar cube. This is because we have a barrier between the swimming pool water and the water inside our cells. This barrier is the membrane or lipid bilayer, it is made of oily compounds. The bilayer is essential it keeps important things in and poisonous things out. All organisms have these bilayers. On their own bilayers would simply block all transport, thus we could not take up nutrients nor could we get rid of waste. Proteins embedded in this membrane are thus needed to act as gate keepers to control movements of ions, nutrients, waste and proteins across the lipid bilayer. These proteins are also the telephone connections between one cell and another. The nerve impulse in humans transmits trigger release of a transmitter (small chemical) from the neuron. The transmitter interacts with another cell by promoting some change in the cell, each cell uses membrane proteins as part of this process. Membrane proteins that control ions movement across the bilayer are called ion channels. They must, like a tap, be able to fully closed to stop leaks but they must also open when required. Many diseases are caused by membrane proteins not working properly. If we are to treat these diseases we need to understand how membrane proteins work. Protein crystallography has transformed our understanding of proteins. It allows us to see every atom in the structure and understand a great deal about the function of the protein. This scientific approach has led to the development of many new drugs. However, this technique can only see one state of the protein at a time. We propose to develop a new approach that will allow us to see in detail exactly how membrane proteins move between the open and closed states. We have chosen to study the pain receptors in humans and the osmotic stress survival proteins in bacteria. These are important systems with obvious medical benefits, treatment of pain and design of new antibiotics.

Technical Summary

Membrane proteins undergo significant conformational changes during their gating. Quantitating these changes is a significant challenge but is vital to our understanding of the molecular biology. We will use EPR in combination with site directed spin labeling to measure these changes. Unpaired electron spins interact with each other over long distances. This can be used to derive the distance between the spins via measurement of the dipolar coupling. For distances up to 15 Å this can be achieved with conventional continuous wave (cw) EPR methods, for distances in the critical 15 to 80 Å regime, pulsed techniques as Pulsed Electron-Electron Double Resonance (PELDOR or DEER) are the method of choice. In the PELDOR time trace, a fixed distance manifests itself as a periodic modulation whose frequency can be converted back into the distance (implemented in the program DEERAnalysis2008). Since the PELDOR experiment is not a single molecule experiment, random intermolecular spin-spin coupling occurs superimposing an exponential decay which has to be removed. However, for this ill-posed back transformation to work reliably and with high precision it is crucial to obtain PELDOR data with observable modulation. We identified several in steps in sample preparation and processing that improve signal to noise and we have obtained preliminary data showing that we can make accurate measurements. We will label the ion channels MscS, MscL, ASIC1a and FaNaC to derive distance measurements in the different conformational states that accompany the closed to open structural transitions and also make meausrements of other crucial states, such desensitisation and inactivation. Making such measurements requires the analysis of selected channel mutants. The PELDOR sudies will be complemented with state-of-the-art measurements of the activity of the mutant channels in the laboratories of the applicants, ensuring that no significant peturbations of structure arise from mutagensis.

Planned Impact

Who will benefit from this research? This research will benefit the biological and medical research communities in both industry and academia. Membrane proteins are a key target for the pharmaceutical industry and UK has a strong record in pharmaceutical and biotechnology research. The academic community recognizes that membrane biology is underdeveloped and holds significant opportunities for future research. How will they benefit from this research? We propose to develop a new integrated approach combining PELDOR (an emerging EPR technology), X-ray crystal analysis, electrophysiology and molecular biology to characterize the conformational states of membrane proteins as they change during function. The genetic basis of over 70% of major diseases has been shown to result from a defect in one or more membrane proteins. Bacterial membrane systems have provided novel targets for therapeutics and it is in this sector of bacterial and fungal pathogenesis that new targets are being discovered as a consequence of more rapid advances in the characterization of membrane proteins. Further, many current therapeutics target membrane proteins as part of their action. For example and directly relevant to this proposal many treatments for high blood pressure (a common ailment) block the sodium channel ENaC. These 'old' drugs were developed before there was any molecular understanding of the channel. There is clear need for new more effective therapies for many diseases and new drugs requiring new scientific understanding. It is likely that the majority of such new drugs will target membrane proteins and their processes. In addition, membrane proteins are also important sensors, diagnostics and biotransformation platforms. Membrane protein biology and biochemistry is therefore an important and impactful area. This proposal will lead to a significant increase in the scientific understanding of ion channel function, transmembrane signaling and membrane transport. By doing this work in the UK we will ensure the impact of the scientific advancement is realized by UK Biotech and Pharmaceutical Industry. What will be done to ensure that they benefit from this research? We will engage with the immediate beneficiaries, (The science community and Health Care Industry) through a mixture of public presentations at companies, professional conferences and to the general public. We will also host workshops at St Andrews in structural biology, membrane functions and in EPR. The structural biology workshop has been running in St Andrews since 1999 and every two years up to 40 PhD students from across the UK come to this week long residential course. The course covers experimental and detailed theory. The two last advanced European Summer Schools on EPR were co-organized by Schiemann (funded by the EU) and trained graduate scientists from across the EU in modern EPR techniques. Such courses ensure the widespread dissemination of new techniques. We will promote public engagement by generating press releases for the University press offices. Our University web sites are an excellent method for the general public to see what research is being carried out with BBSRC funding. We will make ourselves available to international, national and local media organizations to talk about the work. We will manage the regular meetings of the groups involved such that in addition to the science focus, they will also explore ways of communicating the impact of the science to the widest possible audience. The impact of the work will be spearheaded by Liu, Schiemann, Booth and Naismith. The project requires the collaboration of Professor Eric Linguelia (CNRS, Valbone, France), Dr Graham Smith (St Andrews) and Professor Mark Sansom (Oxford). We will collaborate with the UK Membrane Protein Laboratory to ensure the widest possible dissemination of the results to the community. We will also distribute experimental materials (clones and reagents) to other labs.


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Description We have developed a new and reliable method to use spin labelling of membrane proteins to measure distances. This is important in probing their conformational state and thereby their function. We have demonstrated that the method is extremely powerful. Our software is widely used.
Exploitation Route The software and tools that we have developed are freely available. They are already being widely used.
Sectors Chemicals,Pharmaceuticals and Medical Biotechnology

Description Our findings have encouraged the development of PELDOR spectrometry, this has led to investment in this approach more widely.
First Year Of Impact 2016
Sector Chemicals,Digital/Communication/Information Technologies (including Software)
Impact Types Economic

Title Data Underpinning - Accurate Extraction of Nanometer Distances in Multimers by Pulse EPR 
Description NULL 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Description Schools visits 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Each year I host visits to my lab from local secondary school (10's of pupils) and I also give a talk to visiting school pupils on science (approx 50 pupils).

Some of the children seemed to appreciate that chemistry was important in biology.
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014
Description Training and workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Between 20 to 50 pupils per year visit St Andrews and as part of this, they are exposed to structural biology.

Teachers report increased enthusiasm for biomedical science
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010,2011,2012,2013
Description workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Helped in the training of post-graduate students in structural biology at the following meetings.
CCP4/ZCAM workshop, Zaragoza, Spain March 2012
CCP4/ APS workshop, Argonne, USA, June 2012
CCP4/APS workshop, Argonne, USA, June 2013
CCP4/CeBEM workshop, Montevideo, Uruguay, April 2013

Widespread use of UK authored software.
Year(s) Of Engagement Activity 2013,2014