Arthur M. Lesk

Arthur M. Lesk, is an accomplished protein science researcher, who is currently a professor of biochemistry and molecular biology at the Pennsylvania State University, University Park.

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Profile

Lesk has made significant contributions to the study of protein evolution. He and Cyrus Chothia, working at the MRC Laboratory of Molecular Biology in Cambridge, United Kingdom, discovered the relationship between changes in amino-acid sequence and changes in protein structure by analyzing the mechanism of evolution in protein families. This discovery has provided the quantitative basis for the most successful and widely used method of structure prediction, know as homology modelling.

Lesk and Chothia also studied the conformations of antigen-binding sites of immunoglobulins. They discovered the “canonical-structure model” for the conformation of the complementarity-determining regions of antibodies, and they applied this model to the analysis of antibody-germ-line genes, including the prediction of the structure of the corresponding proteins. This work has supported the “humanization” of antibodies for therapy in the treatment of cancer. “This approach to cancer therapy is based on the observation of H. Waldmann that rats can raise antibodies against human cancers, but that the rat antibodies lead to immune responses, similar to allergies, in human patients,” Lesk explains. “Humanization of these antibodies is the formation of hybrid molecules that are more human than rat, but that retain the therapeutic activity while reducing the patient’s immune response.”

Lesk’s work also involves the detailed comparison of proteins in different structural states as a means for understanding the mechanisms that enable the proteins to change conformation, both as part of their normal activity and in disease. The discovery and analysis of these mechanisms was the key to understanding conformation changes in serine protease inhibitors, also known as serpins, mutations of which are an important cause of several diseases, including emphysema and certain types of inherited mental illness.

Lesk used a systematic analysis of protein-folding patterns to develop a mathematical representation that aids in the recognition and classification of these patterns. He also wrote the first computer program to generate schematic diagrams of proteins using molecular graphics, and he developed many algorithms now used by other researchers to analyze the structures of proteins.

Lesk was formerly chair of the Task Group on Biological Macromolecules for the Committee on Data for Science and Technology (CODATA), which aimed to foster worldwide coordination of databases in molecular biology to enhance their quality and utility. He has given invited lectures and presentations related to his research at universities and professional conferences worldwide.

Lesk is a member of the American Physical Society. He has published 189 scientific articles and 8 books related to his research.

Prior to joining Penn State during the fall semester of 2003, Lesk was on the faculty of the clinical school at the University of Cambridge from 1990 to 2003. He was a group leader in the biocomputing program at the European Molecular Biology Laboratory in Heidelberg, Germany, from 1987 to 1990; a visiting scientist at MRC Laboratory of Molecular Biology in Cambridge, United Kingdom, between 1977 and 1990; and a professor of chemistry at Fairleigh Dickinson University in New Jersey from 1971 to 1987. He has held visiting fellowships at the University of Otago in New Zealand and Monash University in Australia. He also is a Life Member of Clare Hall at the University of Cambridge in the United Kingdom.

Along with Karl D. Hardman, Lesk wrote the first computer program for generating the schematic diagram of protein structure. It is known to produce one of the most effective representations of the protein structures and employs the classification scheme for Ribbon Diagrams created by Jane Richardson. Although these schematic diagrams are less detailed compared to the other representations, such as, picture stimulating wire models or space-filling models, it is more effective in presenting the topological relationships among elements of secondary structure and protein, due to its simplistic structural expression.^[1] This was then further improved by creating a program to produce stereoscopic pairs of diagrams. As a result, the viewer’s ability to perceive spatial relationship in complex molecules was enhanced.^[1]

Lesk received a bachelor’s degree, magna cum laude, from Harvard University in 1961. He received his doctoral degree from Princeton University in 1966. He also received a master’s degree from the University of Cambridge in the United Kingdom in 1999.

Operation of the program

The basic operation of the program begins with the execution of line drawing. There are four phases involved in this program:^[2]

1. The input phase – Program reads the input files. There are two input files. They are the coordinates and the details of the contents and appearance of the picture.
2. Picture generation – Geometric transformation of coordinates are generated by the program into picture elements. For example, a cylinder of appropriate size and orientation about the z-axis represents α-helix; each peptide plane is determined for Ribbon Diagrams and β-sheets; and spline fit is used for curved sheets.
3. Hidden-line removal – This step is only required by the cylinders of α-helices and the arrows of β-sheets, not skeletal models. Picture of these structures are classified by three levels of “optical density” – transparent, translucent, or opaque. If lines are passing behind the transparent object, it is not changed. If it passes behind a translucent object, it is altered into dashed lines. If it is opaque, the lines passing through the object are removed completely. This step can be replaced with an alternative step to create a Colour-Raster Output. The lines are ignored and the windows are painted according to the user.
4. Output – Character strings are extended to sets of line segments through a set of stroke tables. Line segments are placed into the two dimensional space.

Miscellaneous

Arthur Lesk's son, Victor Lesk has followed his father into the field of structural biology / bioinformatics, and is currently holds a post-doctoral research position with Michael Sternberg at Imperial College London.

Bibliography

• Introduction to Physical Chemistry (1982) ISBN 9780134927107
• Computational Molecular Biology: Sources and Methods for Sequence Analysis (1988) ISBN 9780198542186
• Protein Architecture: A Practical Approach (1991) ISBN 9780199630554
• Introduction to Protein Architecture (2000) ISBN 9780198504740
• Introduction to Bioinformatics (2002) ISBN 9780199251964
• Introduction to Symmetry and Group Theory for Chemists (2004) ISBN 9781402021503
• Introduction to Protein Science: Architecture, Function and Genomics (2004) ISBN 9780199265114
• Database Annotation in Molecular Biology: Principles and Practice (Editor, 2004) ISBN 9780470856819
• Protein Structure Prediction: Concepts and Applications (with Anna Tramontano, 2006) ISBN 9783527311675
• Introduction to Genomics (2007) ISBN 9783527311675

References

1. ^ ^{a b} Lesk, Arthur M. Hardman, Karl D. Computer-Generated Schematic Diagrams of Protein Structures. Science 216:539-540, 1982
2. ^ Lesk, Arthur M. Hardman, Karl D. Computer-Generated Pictures of Proteins. Methods in Enzymology. 115: 381-389.