Bacteria display a variety of proteins on their surfaces which play important roles in the biology of the organism. Some are involved in uptake of nutrients, whereas others can act as antigens and play a part in the infection of human cells. The overall aim of my work is to understand the structures of these proteins, how they work and how they interact with the molecules of the human immune system. To do this we use a range of physical techniques, including X-ray crystallography and NMR, which provide us with an atomic level description of protein structure. This type of work then has a natural translation into applications in the area of vaccines. For example, I am currently working with colleagues on a new approach to the development of a vaccine against meningococcal meningitis.

I am currently Professor of Molecular Microbiology, working within the Microbiology Research Grouping in the Faculty. I obtained my first degree, and then PhD, from the University of Cambridge, before moving on to work in Prof Bill Shaw's group in Leicester. This gave me a background in the use of structural analysis in the study of protein function, as applied to the enzyme chloramphenicol acetyltransferase (CAT). I then obtained a Postdoctoral Research Fellowship from the Wellcome Trust, to work on the antibody-binding protein, Protein G, from Streptococcus, which is widely used in affinity resins for purifying antibodies. Working with Gordon Roberts and Lu-Yun Lian in the Biological NMR Centre in Leicester, we published the first description of the structure of this important protein. Working with Dale Wigley, we also determined the crystal structure of a Protein G domain bound to an Fab fragment, revealing the molecular basis for its recognition of antibody (Nature 359, 752-754). This started my interest in bacterial cell surface proteins- the structures they adopt, how they function and interact with the immune system. In 1993, I moved to UMIST as a lecturer, and have been at Manchester ever since. At this time, I started to work on the outer membrane proteins (OMPs) from Neisseria meningitidis, the causative agent of meningococcal meningitis. This work was initially funded through a Lister Fellowship, which I held between 1996 and 2001. Working with Mark Achtman's lab in Berlin, we were the first group to publish a crystal structure of an outer membrane protein from Neisseria, the OpcA protein (PNAS 99, 3417-3421). In parallel, I also investigated the interaction of the immune system with Neisserial OMPs, through collaborations with Martin Maiden (Oxford) and Ian Feavers (NIBSC). OMPs such as the PorA porin have been shown to provide protective immunity against meningococcal meningitis, and have been used as constituents of vaccines against the disease. This work has recently translated into Wellcome Trust Translation Award with Andrew Pollard (Oxford), Martin Maiden and Ian Feavers, aiming to develop a new approach to immunization against meningococcal disease. My lab has also focused on the biogenesis of type IV pili in Gram negative bacteria. Type IV pili play major roles in bacterial cell adhesion, DNA transformation and motility. They are assembled through the action of a complex group of proteins which span the inner and outer membranes, acting effectively as a macromolecular machine. In a collaboration with Tone Tonjum in Oslo and Bob Ford's group in Manchester, we have worked on the characterisation of the PilQ outer membrane secretin by electron microscopy (J Biol Chem 279, 39750-39756), revealing an unusual chamber-like structure which mediates the passage of type IV pili across the outer membrane. More recent work has concentrated on the determination of the structures of the component proteins within the assembly machine (eg J Mol Biol 364, 186-195) and earlier this year we published the first crystal structure of a complex between two type IV pilus assembly proteins (J Biol Chem 286, 24434-42).

I have always maintained a strong interest in commercial and industrial applications of my work. I was a co-founder, with Prof Bill Shaw and Drs Bill Primrose and Ann Lewendon, of a biotechnology/ pharmaceutical start-up company called PanTherix in 1997. More recently, I obtained a grant from BBSRC under the Bioprocessing Research Industry Club (BRIC) initiative, working with Jim Warwicker in my Faculty and Robin Curtis in Chemical Engineering. Our aim is to investigate better methods for understanding and predicting protein aggregation, which is a significant problem in the bioprocess industry.

Aggregation of biotherapeutic proteins- mechanism and effects on the immune response

Therapeutic protein drugs (eg monoclonal antibodies) are now well established in the treatment of many major human diseases, and constitute the most rapidly expanding class of drugs within the portfolio of most, if not all, of the major global pharmaceutical companies. Administration of recombinant human therapeutics can, however, lead to the production of anti-drug antibodies which impair drug function and, although less commonly, can lead to serious adverse health effects. The elimination, or at least reduction, of unwanted immune responses to biotherapeutics is therefore a priority within the bioprocess and biopharmaceutical industries. The presence of aggregates within biopharmaceutical preparations is a matter of concern, particularly how aggregates engage with the immune system and how this might fuel undesirable downstream immunogenicity. One approach is to use a range of biophysical and computational methods to examine how aggregation occurs in therapeutic proteins. This is an interdisciplinary collaboration, with Robin Curtis in Chemical Engineering, Jim Warwicker and Alexander Golovanov in Chemistry, and Alain Pluen in Pharmacy. We hope to obtain a greater understanding of the way in which the structure, solution conditions and dynamics impact on aggregation.  We are also examining how aggregation impacts on the nature and vigour of the immune response. Recent data, collected as part of a collaboration with Ian Kimber and Rebecca Dearman in the Faculty, suggests that aggregation causes a Th1 skewing (Ratanji et al.  Toxicol. Sci. 153, 258-270). We are also interested in the role which trace contaminants of remaining host cell proteins might influence the response (see Ratanji et al. Immunology, in press). Clearly, this work has direct relevance to the bioprocess industry, and we are currently working with several pharmaceutical companies in these areas.

Integral outer membrane proteins from Neisseria- from fundamental studies to vaccine components
Neisseria meningitidis is the causative agent of bacterial meningococcal meningitis and septicaemia, and is a significant public health problem in developed and developing countries. I have worked for many years towards an understanding the structure and assembly of the cell surface proteins from this organism (eg Marsay et al J Infect 71, 326-337; Saleem et al. PloS ONE 8 e0056746). Current work is aimed at using that information to develop improved vaccines against the disease. We seek to integrate protein structural studies with antigen design, through use of novel protein assemblies and scaffolds for antigen presentation.

Understanding type IV pilus assembly and natural competence in Gram-negative bacteria
Type IV pili are complex polymers, made up principally of a major pilin subunit, which extend 1-2μm from the surface of the bacterium. They are the most widespread fimbrial assembly found in Gram-negative bacteria, and are known to play important roles in cell adhesion, DNA uptake and motility. The property of twitching motility, in particular, is dependent on the rapid retraction of pili, a process which is capable of generating a powerful mechanical force. The process of pilus assembly and disassembly is driven by a powerful macromolecular machine, consisting of a complex of several proteins which span the inner and outer membranes. A fascinating aspect of type IV pili is their relationship to natural competence- the ability of bacteria to take up DNA from the external environment. Our general aim is to use a range of biochemical and biophysical methods to study how this process works at the molecular level (eg Karuppiah et al 2016 J Struct Biol. In press;  Karuppiah et al 2014 J Biol Chem 289, 33187-97; Karuppiah et al 2013 PNAS pnas.1312313110; Karuppiah & Derrick 2011 J Biol Chem 286, 24434-24442)

I have been Chair of the Biosciences Education Board within the Faculty, which has responsibility for over half of the degree programmes which we offer. I teach on several different lecture units, covering my research interests in bacterial surface membrane proteins, secretion and methods for the study of protein structure. I also act as an academic advisor to a Microbiology tutorial group.