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Protein linguistics — a grammar for modular protein assembly?

Nature Reviews Molecular Cell Biology volume 7, pages 68–73 (2006)Cite this article

Abstract

The correspondence between biology and linguistics at the level of sequence and lexical inventories, and of structure and syntax, has fuelled attempts to describe genome structure by the rules of formal linguistics. But how can we define protein linguistic rules? And how could compositional semantics improve our understanding of protein organization and functional plasticity?

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Figure 1: Grammatical hierarchies.
Figure 2: The Rosetta Stone.
Figure 3: Generation of a novel lexical protein entry.

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Acknowledgements

I wish to thank M. C. Baker and M. Sudol for critically commenting on this manuscript, and the members of the Protein Modules Consortium for inspiring discussions. The author is supported by a Marie Curie Excellence Grant of the Framework Program 6 of the European Union.

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Authors and Affiliations

  1. the Department of Cell Biology and Oncology, Consorzio Mario Negri Sud, Marie Curie Unit of Actin Cytoskeleton Regulation, Via Nazionale 8A, Santa Maria Imbaro, 66030, Italy

    Mario Gimona

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DATABASES

Artificial Intelligence and Molecular Biology (electronic text (PDF) of the out-of-print book)

Cytoscape

FEBS workshop on Modular Protein Domains: from functional plasticity to protein linguistics (official meeting web site)

Protein Modules Consortium

The BIND interaction database

The DIMA domain interaction map

The InterPro database

The MINT database

The Seefeld Convention

FURTHER INFORMATION

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Glossary

Affix

A meaningful element that cannot stand on its own but it is added to another element.

Automaton

A device that reads input, conventionally from left to right, and either recognizes or generates language.

Clause

A basic unit of grammatical structure that expresses a single thought.

Grammar

The part of a language that is responsible for assembling basic words into larger words, phrases and clauses in systematic ways. For simplicity, grammar may be viewed as a combination of syntax and morphology.

Lexica

The stocks of basic words.

Linguistics

The study of the nature, structure and variation of language (includes the sub-disciplines of morphology, syntax, semantics and pragmatics).

Module

Different languages have different concepts of a module but there are several shared ideas. Modules are similar to objects in an object-orientated language, although a module might contain many procedures and/or functions, which would correspond to many objects. In computer science, modules are described as a portion of a program that carries out a specific function and might be used alone or combined with other modules of the same program.

Phrase

A group of words that appear next to each other or stay together in the arrangement of a sentence and that form a syntactic unit.

Prefix

A meaningful element that cannot stand on its own but it is added to the beginning of another element.

Root

The core of a word, before prefixes and suffixes are attached.

Semantics

The branch of linguistics concerned with the meaning of linguistic expression.

Sentence

A basic unit of a language that expresses a complete thought.

Stem

Prefixes and suffixes attach to a stem in order to form a longer word.

Suffix

A meaningful element that cannot stand on its own but it is added to the end of another element.

Syntax

The branch of linguistics that studies how words are combined to make phrases and sentences.

Word

A freestanding portion of language with a coherent meaning.

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Gimona, M. Protein linguistics — a grammar for modular protein assembly?. Nat Rev Mol Cell Biol 7, 68–73 (2006). https://doi.org/10.1038/nrm1785

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