Internal

Bioinformatics analysis of snake venom proteins

Use of bioinformatics techniques to find sequences of snake venom serine proteases and study their structure and function.

Department: Biomolecular Sciences, Biological Sciences

Supervised by: Dr E. Gail Hutchinson

The Placement Project

Snake venoms contain a complex mixture of proteins and peptides. One major family of enzymes found in the venoms of viper snakes is serine proteases. These interfere with various stages of blood coagulation, causing either abnormal blood clotting or excessive bleeding in victims of snake bites. An understanding of the structures and functions of these enzymes may lead to improved treatments for snake bites. These molecules are also potential candidates for treating haemostatic disorders such as heart attacks and strokes. The aim of this placement is to use bioinformatics techniques to further our understanding of this important family of enzymes. The first stage involves updating our existing database of viper venom serine proteases (currently 150 sequences) and their functions to generate an up-to-date resource about all known viper venom serine proteases. A phylogenetic tree will be generated to study the relationships between the serine proteases of different functions in different snakes. The second aim of the project is to study an interesting set of serine proteases which have been found in venoms from non-viper snakes and lizards. These proteins will be compared with each other and with viper venom serine proteases to identify common and distinctive features in their sequences and structures. This project follows on from a successful PhD project in the area. Much of the groundwork has been done and the project is at an ideal stage for a placement student to obtain interesting results in a short time frame and hopefully be an author on a publication.

Tasks

The project will be computer based, with the students using bioinformatics programs to obtain and analyse information. Some bioinformatics programs such as BLAST and ClustalW will be familiar to students; other programs for performing phylogenetic analysis and predicting structures will also be used. Some literature study will be needed to identify functions of new serine proteases identified.

Skills, knowledge and experience required

The student should have good general computer skills. Ideally some experience of using basic bioinformatics programs such as BLAST would be beneficial, however this is not essential and training can easily be provided.

Skills which will be developed during the placement

The student will have the opportunity to develop enhanced skills in bioinformatics which should be very useful both in part 3 projects and in future employment. It is hoped that the placement will lead to authorship on a publication resulting from the research. Bioinformatics skills are only taught briefly during the formal undergraduate programme so this placement provides a valuable opportunity to obtain experience of using a wider range of bioinformatics programs in a genuine research setting. The programs used will include sequence comparison tools and also programs for predicting protein structures.

Place of Work

Harborne Building, School of Biological Sciences

Hours of Work

9-5

Approximate Start and End Dates (not fixed)

Unknown - Unknown

How to Apply

students should apply with a CV and covering letter to Dr Gail Hutchinson, School of Biological Sciences Harborne Building.


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