Science Literature

Nature 438, 504-507 (24 November 2005)

Design principles of a bacterial signalling network

Markus Kollmann, Linda Lovdok, Kilian Bartholome, Jens Timmer1, and Victor Sourjik

Abstract: Cellular biochemical networks have to function in a noisy environment using imperfect components. In particular, networks involved in gene regulation or signal transduction allow only for small output tolerances, and the underlying network structures can be expected to have undergone evolution for inherent robustness against perturbations. Here we combine theoretical and experimental analyses to investigate an optimal design for the signalling network of bacterial chemotaxis, one of the most thoroughly studied signalling networks in biology. We experimentally determine the extent of intercellular variations in the expression levels of chemotaxis proteins and use computer simulations to quantify the robustness of several hypothetical chemotaxis pathway topologies to such gene expression noise. We demonstrate that among these topologies the experimentally established chemotaxis network of Escherichia coli has the smallest sufficiently robust network structure, allowing accurate chemotactic response for almost all individuals within a population.

Revealing the mystery of the bacterial flagellum:
A self-assembling nanomachine with fine switching capability
JAPAN NANONET BULLETIN - 11th Issue - February 5, 2004

Keiichi NAMBA
Professor, Graduate School of Frontier Biosciences, Osaka University
(Issued in Japanese: March 25, 2003)

(the online article contains links to many fasinating animations of the bacterial flagellum)

Nature created a rotary motor with a diameter of 30 nm. Motility of bacteria, such as Salmonella and E. coli with a body size of 1 to 2 micron, is driven by rapid rotation of a helical propeller by such a tiny little motor at its base. This organelle is called the flagellum, made of a rotary motor and a thin helical filament that grows up to about 15 micron. It rotates at around 20,000 rpm, at energy consumption of only around 10 to 16 W and with energy conversion efficiency close to 100 percent. Prof. Nambas research group is going to reveal the mechanism of this highly efficient flagellar motor that is far beyond the capabilities of artificial motors.

The flagellum is made by self-assembly of about 25 different proteins. The rotor ring made of protein FliF is the first to assemble in the cytoplasmic membrane. Then, other protein molecules attach to the ring one after another from the base to the tip to construct the motor structure. After the motor has been formed, the flagellar filament, which functions as a helical propeller, is assembled. Precise recognition of the template structure by component proteins allows this highly ordered self-assembly process to proceed without error. The flagellar filament is made of 20,000 to 30,000 copies of flagellin polymerized into a helical tube structure. Flagellin molecules are transported through a long narrow central channel of the flagellum from the cell interior to the distal end of the flagellum, where they self-assemble in a helical manner by the help of a cap complex. The cap is pentameric complex made of HAP2 and has a pentagonal plate and five leg domains, whose flexible stepping movements accompanied by rotation of the whole cap is the key mechanism to promote the efficient self-assembly of flagellin molecules by preparing just one binding site of flagellin at a time and guiding the binding.

This article recently published in Accounts of Chemical Research discusses some key considerations for understanding how proteins bind in cellular machines, and offers a new approach to predicting binding. It provides some of the quantitative basis needed for putting irreducible complexity on a quantitative basis. Notably the authors seek to document the effect of mutations on reduced specificity of binding: "We have found that introducing mutations can significantly reduce specificity by introducing an additional binding mode." which reduction in specificity would be the first stage in the failure of a reducibly complex machine.

Worth reading both by those looking at the biochemistry and biology of protein machines and those pursuing the probability arguments of Intelligent Design.

Acc. Chem. Res., ASAP Article 10.1021 ar040204a S0001 4842(04)00204 3
Web Release Date: October 15, 2005
Copyright 2005 American Chemical Society
Mechanisms of Protein Assembly: Lessons from Minimalist Models
Yaakov Levy and Jose N. Onuchic
Center for Theoretical Biological Physics, Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093

Received May 26, 2005

Abstract:
Many cellular functions rely on interactions among proteins and between proteins and nucleic acids. The limited success of binding predictions may suggest that the physical and chemical principles of protein binding have to be revisited to correctly capture the essence of protein recognition. In this Account, we discuss the power of reduced models to study the physics of protein assembly. Since energetic frustration is sufficiently small, native topology-based models, which correspond to perfectly unfrustrated energy landscapes, have shown that binding mechanisms are robust and governed primarily by the protein's native topology. These models impressively capture many of the binding characteristics found in experiments and highlight the fundamental role of flexibility in binding. The essential role of solvent molecules and electrostatic interactions in binding is also discussed. Despite the success of the minimally frustrated models to describe the dynamics and mechanisms of binding, the actual degree of frustration has to be explored to quantify the capacity of a protein to bind specifically to other proteins. We have found that introducing mutations can significantly reduce specificity by introducing an additional binding mode. Deciphering and quantifying the key ingredients for biological self-assembly is invaluable to reading out genomic sequences and understanding cellular interaction networks.

Introduction
The life of cells is orchestrated by a network of chemical reactions involving numerous proteins and nucleic acids and the transport of those molecules between cellular compartments. The remarkable efficiency of organizing these processes to yield a cellular function presents a major theoretical puzzle given the large number of molecular species and the crowded environment they inhabit. In the recent years, we have come to understand the assembly of the individual actors in this drama thanks to many cooperative efforts between experiments and theory. We now understand the main principles of folding kinetics[1,2] can often predict monomeric protein structure[3] and can even design novel protein structures.[4] However, knowing everything about isolated monomeric proteins does not give a complete understanding of function. Function requires change of structure and specific recognition to form large assemblies. These processes must be governed by the information stored in their sequences and structures. Furthermore, biomacromolecules are flexible with a rich repertoire of movements on various length and time scales. These motions are essential to determine the ability of a protein to bind different ligands at the same or different binding sites.[5,6] Deciphering the molecular and structural origins of high specificity as well as the catalytic promiscuity and multitasking of proteins is prerequisite for a quantitative understanding of the complexity and multidimensionality in genomes. This cooperation of many proteins and nucleic acids, which is largely "wireless", is quite intricate. Understanding the principles of biomolecular assembly in quantitative detail constitutes the basis for the molecular theory of biological networks.

Theoretical and computational studies of protein binding have concentrated on analyzing the structural and chemical properties of interfaces[7,8] as well as predicting the structure of the formed complexes and their binding affinity.[9,10] Understanding the organization of proteins into large complexes is required to understand their function and irreversible aggregation. The challenge of predicting the complex formed between pairs of proteins has been addressed for several years by docking two proteins using various models, which range from reduced models11[12] to atomistic ones[9] and include different flavors. Approaches to predict the structures of higher complexes, which are often defined as cellular machines, have been recently developed too. These approaches include, for example, combinatorial docking schemes[13] or fitting to cryo density maps at low resolution.[14] Some progress has been made in recent years in the performance of docking algorithms, yet their successes in predicting the structure of the protein complex are limited mainly to docking of the bound conformations of the complex subunits.

The inferiority of binding prediction to folding prediction is surprising because the conformational search required in binding processes of two folded proteins is smaller than that involved in protein folding. This shortcoming suggests that the physical and chemical principles of protein binding have to be revisited. The poor predictions of docking when using the conformations of the free subunits obviously indicates that protein flexibility is an important component in binding. Several docking approaches have introduced side-chain flexibility by using a rotamers library; however, it seems that backbone flexibility cannot be ignored.[15] It is likely, thus, that flexibility effects are still grossly underestimated as suggested from our recent association studies.[16-18] Solvent is also a critical component in protein association. While the protein cores are usually dry and contain a few water molecules, the interfaces in protein complexes are often very wet[19] (see Figure 1). Recently, it was found that a funneled potential for binding between proteins was obtained only upon solvation of assembly interfaces.[20] These observations provide a strong indication that water can be indispensable in protein assembly and undoubtedly in protein binding to DNA due to its highly charged surface.

This is from a Letter to Nature in the October 6, 2005 issue.

Nature 437, 862-865 (6 October 2005)

Microscopic artificial swimmers

Remi Dreyfus, Jean Baudry, Marcus L. Roper, Marc Fermigier, Howard A. Stone and Jerome Bibette

Abstract: Microorganisms such as bacteria and many eukaryotic cells propel themselves with hair-like structures known as flagella, which can exhibit a variety of structures and movement patterns. For example, bacterial flagella are helically shaped and driven at their bases by a reversible rotary engine, which rotates the attached flagellum to give a motion similar to that of a corkscrew. In contrast, eukaryotic cells use flagella that resemble elastic rods and exhibit a beating motion: internally generated stresses give rise to a series of bends that propagate towards the tip. In contrast to this variety of swimming strategies encountered in nature, a controlled swimming motion of artificial micrometre-sized structures has not yet been realized. Here we show that a linear chain of colloidal magnetic particles linked by DNA and attached to a red blood cell can act as a flexible artificial flagellum. The filament aligns with an external uniform magnetic field and is readily actuated by oscillating a transverse field. We find that the actuation induces a beating pattern that propels the structure, and that the external fields can be adjusted to control the velocity and the direction of motion.

Cell Biology International
Volume 28, Issue 11 , November 2004, Pages 729-739

Copyright © 2004 International Federation for Cell Biology Published by Elsevier Ltd.
Chance and necessity do not explain the origin of life

J.T. Trevors(a) and D.L. Abel(b)

(a)Laboratory of Microbial Technology, Department of Environmental Biology, Room 3220, Bovey Building, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
(b)The Gene Emergence Project, The Origin-of-Life Foundation Inc., 113 Hedgewood Dr., Greenbelt, MD 20770-1610, USA

Received 8 April 2004; revised 19 May 2004; accepted 24 June 2004. Available online 17 November 2004.

Abstract
Where and how did the complex genetic instruction set programmed into DNA come into existence? The genetic set may have arisen elsewhere and was transported to the Earth. If not, it arose on the Earth, and became the genetic code in a previous lifeless, physical–chemical world. Even if RNA or DNA were inserted into a lifeless world, they would not contain any genetic instructions unless each nucleotide selection in the sequence was programmed for function. Even then, a predetermined communication system would have had to be in place for any message to be understood at the destination. Transcription and translation would not necessarily have been needed in an RNA world. Ribozymes could have accomplished some of the simpler functions of current protein enzymes. Templating of single RNA strands followed by retemplating back to a sense strand could have occurred. But this process does not explain the derivation of “sense” in any strand. “Sense” means algorithmic function achieved through sequences of certain decision-node switch-settings. These particular primary structures determine secondary and tertiary structures. Each sequence determines minimum-free-energy folding propensities, binding site specificity, and function. Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic – that is, it is programmatically and algorithmically organized and controlled.

Keywords: Cellular communication; Chance; Necessity; Genetic control; DNA; RNA; Evolution; Information theory; Life origin; Astrobiology; Panspermia

Biological Reviews (2005), :1-24 Cambridge University Press Copyright C 2005 Cambridge Philosophical Society DOI 10.1017/S1464793104006657

Review Article

Why repetitive DNA is essential to genome function

James A. Shapiro and Richard von Sternberg

Abstract

There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells.

Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes.

Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring.

Employing an information science model, the 'functionalist'
perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.

(Key Words: transposable element; non-coding DNA; satellite DNA; junk DNA; transcriptional regulation; chromatin domains; evolution; biocomputing; systems biology; data storage.