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Next-generation protein engineering: integration of ab-initio modelling, high-throughput screening and structural fingerprinting by mass spectrometry


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Key facts

Type of research degree
Application deadline
Ongoing deadline
Country eligibility
UK and EU
Competition funded
Source of funding
University of Leeds
Dr Emanuele Paci and Professor Frank Sobott
Additional supervisors
Darren Tomlinson
School of Molecular and Cellular Biology
Research groups/institutes
<h2 class="heading hide-accessible">Summary</h2>

Recombinant proteins are playing an ever-increasing role as therapeutics and reagents. High-affinity binding candidates can be produced in a high-throughput manner through the process of selection and evolution from large libraries. Unfortunately, the structures of the complexes with target protein can only be determined for a small number of them in a costly, low-throughput manner, typically by x-ray crystallography. Reliable modeling of complexes would greatly help to understand their mode of action and improve them by further engineering.

<h2 class="heading hide-accessible">Full description</h2>

<p>Specifically, Affimers are designed proteins that can be used to probe function of target proteins that bind at specific binding hot-spots. They are currently used for a number of purposes, such as identifying potentially druggable regions on protein surfaces.<br /> The project consists in developing, applying and experimentally validating rational methods to identify the binding of Affimer reagents on target proteins.</p> <p>Experimental approach: Based on our previous work we will develop a procedure to predict the structures of unknown complexes that requires only the sequence of an Affimer and a structure of the unbound target. The expected limit of such procedure is that multiple models will be obtained due to the flexibility of both binding partners. Key to the project is use of advanced biophysical techniques based on mass spectrometry to select and validate the correct model. The approach will be applied to known Affimers that bind and inhibit Ras (for which some structures are available and will provide a training set for the modelling method), as well as Affimers that effect Ras function in different ways. Currently available crystal structures demonstrate that the anti-Ras Affimers are binding to two distinct regions on Ras; one is a previously identified shallow pocket which block nucleotide exchange, and the other has identified a novel Ras conformer and a much deeper druggable pocket that block nucleotide exchange and binding to downstream effectors.</p> <p>&nbsp;</p>

<h2 class="heading">How to apply</h2>

<p>Formal applications for research degree study should be made online through the&nbsp;<a href="">University&#39;s website</a>. Please state clearly in the research information section&nbsp;that the research degree you wish to be considered for is &ldquo;Next-generation protein engineering: integration of ab-initio modelling, high-throughput screening and structural fingerprinting by mass spectrometry&rdquo;as well as <a href="">Dr Emanuele Paci </a>as your proposed supervisor.</p> <p>If English is not your first language, you must provide evidence that you meet the University&#39;s minimum English language requirements (below).</p> <p><em>We welcome applications from all suitably-qualified candidates, but UK black and minority ethnic (BME) researchers are currently under-represented in our Postgraduate Research community, and we would therefore particularly encourage applications from UK BME candidates. All scholarships will be awarded on the basis of merit.</em></p>

<h2 class="heading heading--sm">Entry requirements</h2>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

<h2 class="heading heading--sm">English language requirements</h2>

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<h2 class="heading">Funding on offer</h2>

<p>Candidates are encouraged to apply for Leeds Doctoral Scholarship (April deadline)</p>

<h2 class="heading">Contact details</h2>

<p>For further information please contact the Graduate School Office<br /> e: <a href=""></a> , t: +44 (0)113 343 8186</p>