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A mathematical approach to protein biophysics. (English) Zbl 1390.92003

Biological and Medical Physics, Biomedical Engineering. Cham: Springer (ISBN 978-3-319-66031-8/hbk; 978-3-319-66032-5/ebook). xi, 290 p. (2017).
The book is intended for a target audience comprising of mathematicians with interdisciplinary interests in chemistry and physics whose main aim is a better understanding of molecular details in order to improve the development of models; the series of eighteen chapters provides a background in protein biochemistry and biophysics coupled with a rule-based description of molecular interactions. The book has already been used for both undergraduate and graduate courses, highlighting the adequacy of coupling the description of theoretical concepts with exercises and extensive references for further reading.
The first chapter provides a brief overview of the book and how it should be used to maximise its efficiency. In the second chapter the authors present a set of modelling-based rules for proteins, focusing on describing the digital nature of molecules with an emphasis on the ionic rules and the carbon/hydrogen rules, as well as the consequences of hydrophobicity and hydrophilicity; as a resource for modelling, the Pchemomics term is coined and the protein database (PDB) briefly described. Next, a short overview of multi-scale models is followed by the description of hydrophobic interactions focused on the dynamics of dehydrons. The third chapter is built on the detailed description of electrostatic forces and includes information on (i) the characteristics of direct bonds such as covalent, ionic or hydrogen bonds, (ii) the charge-force relationship, (iii) interactions involving dipoles, (iv) van der Walls forces and (v) induced dipoles. In the fourth chapter, the authors present protein basics starting with a description of amino acids, of the special bonds which characterize them and the expected post-translational modifications. A detailed overview of special side chains such as glycine, proline, arginine, lysine and cysteine precedes a discussion on amino acids frequencies in the context of PDB. The fifth chapter focuses on protein structure, introducing the concepts of primary and secondary structures; also included is an overview of the mechanical properties of proteins and the elements and usage of the Ramachandran plot. The sixth chapter is built on the summary of hydrogen bonds, reviewing the possible types and the geometric criteria for their classification based on the hydrogen positions (fixed, variable or ambiguous). In the seventh chapter, the authors present the composition of protein-protein interfaces based on the hydrophobic interactions and the amino acids and potential pairs at protein-protein interfaces. Next, the wrapping of electrostatic bonds is introduced; the role of nonpolar groups and methods for assessing polarity in counting residues are described in detail. The eighth chapter concludes with a review of dynamic models and the interpretation of the genetic code. The ninth chapter focuses on the description of the stickiness of dehydrons concentrating on the role of the surface adherence force and the effect of membrane morphology. The two-zone model (boundary zone and diffusion zone) and the kinetic model of morphology are described in detail. The tenth chapter is built on details of electrostatic forces; the dipole-dipole interactions, charged interaction and quadrapole potential are presented at large.
In the eleventh chapter, the role of dehydrons in protein interactivity is presented. The description of the role of dehydrons in antibody-antigen associations or in quaternary structural assemblages is followed by a discussion on hydrophobic contacts. The twelfth chapter is built on the description of aromatic interactions and focuses on the partial charge model and the aromatic-polar and aromatic-aromatic interactions. In the thirteenth and fourteenth chapters, the authors present antibody-antigen complexes and methods for evaluating peptide bond rotation and evaluating (and predicting) their effect on protein folding. The fifteenth chapter reviews continuum equations for electrostatics particularly applicable to dielectric materials. Also included are computational techniques and models for local and nonlocal dielectrics. In the sixteenth chapter, elements of the wrapping technologies are presented with a focus on imatinib resistance and its side-effects. The last two chapters seventeen and eighteen consist of a summary of future directions of research followed by an overview of the units used throughout the book (both basic unit and derived units)
The book is built in a textbook-like manner, each chapter being followed by exercises to reinforce the concepts presented throughout. Also included is a comprehensive list of references offering multiple options for future reading. The style of the book makes it accessible to a wide range of audiences from students to established researchers. Although written with a specialised audience in mind, the numerous examples make it accessible to researchers with multidisciplinary backgrounds.

MSC:

92-02 Research exposition (monographs, survey articles) pertaining to biology
92D20 Protein sequences, DNA sequences
92B05 General biology and biomathematics
92C05 Biophysics
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