PDF《arXiv:0705.1845v1 [physics.bio-ph]》

arXiv:0705.

1845v1 [physics.bio-ph]

13 May

2007 Introduction to protein folding for physicists Pablo Echenique? Theoretical Physics Department, University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain. Institute for Biocomputation and Physics of Complex Systems (BIFI), Edi?cio Cervantes, Corona de Arag? on 42, 50009, Zaragoza, Spain. February 1,

2008 Abstract The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of ?exible molecules is noth- ing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them power- ful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the ?rst steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day sta- tus of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we phys- ically de?ne the problem stating the assumptions behind this (commonly implicit) de?nition. Finally, we review the '

special ?avor'

of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.

1 Why study proteins? Virtually every scienti?c book or article starts with a paragraph in which the writer tries to persuade the readers that the topic discussed is very important for the future of humankind. We shall stick to that tradition in this work;

but with the con?dence that, in the case of proteins, the persuasion process will turn out to be rather easy and automatic. ?E-mail address: [email protected] ― Web page: http://www.pabloechenique.com

1 Proteins are a particular type of biological molecules that can be found in every single living being on Earth. The characteristic that renders them es- sential for understanding life is simply their versatility. In contrast with the relatively limited structural variations present in other types of important bio- logical molecules, such as carbohydrates, lipids or nucleic acids, proteins display a seemingly in?nite capability for assuming di?erent shapes and for producing very speci?c catalytic regions on their surface. As a result, proteins constitute the working force of the chemistry of living beings, performing almost every task that is complicated. Quoting the ?rst sentence of a section (which shares this section'

s title) in Lesk'

s book [1]: In the drama of life on a molecular scale, proteins are where the action is. Just to state a few examples of what is meant by '

action'

, in living beings, proteins ? are passive building blocks of many biological structures, such as the coats of viruses, the cellular cytoskeleton, the epidermal keratin or the collagen in bones and cartilages;

? transport and store other species, from electrons to macromolecules;

? as hormones, transmit information and signals between cells and organs;

? as antibodies, defend the organism against intruders;

? are the essential components of muscles, converting chemical energy into mechanical one, and allowing the animals to move and interact with the environment;