Modeling Macromolecular Complexes: A Journey Across Scales - Modeling in Computational Biology and Biomedicine - page 1

Chapter 1
Modeling Macromolecular Complexes:
A Journey Across Scales

Frederic Cazals, Tom Dreyfus, and Charles H. Robert

1.1 Introduction

Proteins and nucleic acids thoroughly pervade biological organisms. Fully appre-
ciating biological development and pathologies implies understanding the nature
of these macromolecules in detail. But if macromolecules are the fundamental
components of an organism, then Biology itself is based on their mutual interactions.
For example, a receptor complex that spans the cell membrane may be activated
by binding a hormone on the outside of a cell, and only then interact with a
partner protein on its inner-membrane side in the cell to trigger a signaling cascade.
The biological interactions we address in this chapter are direct and physical,
involving formation of a transient or permanent complex. In the signaling system
just mentioned, the binding of the hormone, and of the partner protein afterwards,
create transient complexes. In contrast, when 50 proteins and numerous nucleic
acids assemble to make a ribosome [ 64 ], which is responsible for physically
translating the genetic code into new proteins, the resulting machine is more
permanent. Another example of a long-lived structure is the nuclear pore complex
(NPC), made up of about 450 proteins, which allows active transport of molecules
from the nucleus to the cytoplasm in eukaryotic cells and vice-versa.

F. Cazals ( ) · T. Dreyfus
Inria Sophia Antipolis Mediterranee, ABS project-team, 2004 Route des Lucioles, 06902, Sophia
Antipolis, France
e-mail: [e-mail] ; [e-mail]
C.H. Robert
Laboratoire de Biochimie Theorique - UPR 9080 CNRS, Institut de Biologie Physico Chimique,
Universite Paris Diderot Sorbonne Paris Cite, 13 rue Pierre et Marie Curie, 75005, Paris, France
e-mail: [e-mail]