Protein-polymer nano-machines. Towards synthetic control of biological processes

Abstract

The exploitation of nature's machinery at length scales below the dimensions of a cell is an exciting challenge for biologists, chemists and physicists, while advances in our understanding of these biological motifs are now providing an opportunity to develop real single molecule devices for technological applications. Single molecule studies are already well advanced and biological molecular motors are being used to guide the design of nano-scale machines. However, controlling the specific functions of these devices in biological systems under changing conditions is difficult. In this review we describe the principles underlying the development of a molecular motor with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for control of the motor function. The molecular motor is a derivative of a TypeI Restriction-Modification (R-M) enzyme and the synthetic polymer is drawn from the class of materials that exhibit a temperature-dependent phase transition.The potential exploitation of single molecules as functional devices has been heralded as the dawn of new era in biotechnology and medicine. It is not surprising, therefore, that the efforts of numerous multidisciplinary teams 12. have been focused in attempts to develop these systems. as machines capable of functioning at the low sub-micron and nanometre length-scales 3. However, one of the obstacles for the practical application of single molecule devices is the lack of functional control methods in biological media, under changing conditions. In this review we describe the conceptual basis for a molecular motor (a derivative of a TypeI Restriction-Modification enzyme) with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for controlling the motor function 4.

Figure 1

DNA Translocation by TypeI Restriction-Modification enzyme. The yellow block represents the recognition sequence for the enzyme. The enzyme binds at this site and upon addition of ATP, DNA translocation begins. During translocation, an expanding loop is produced.

Figure 2

Schematic of the motor subunits. HsdS denotes the DNA binding subunit; HsdM – is the subunit responsible for DNA methylation and HsdR subunit, together with the core enzyme acts to restrict DNA.

Figure 3

Mechanism of DNA cleavage. The enzyme subunits are represented by: green ellipse – M2S complex, green box – HsdR subunit (with ATPase and restrictase activities; C denoting cleavage site). The black line represents DNA with the yellow box denoting the recognition sequence. Arrow shows direction of DNA translocation. For more details see text.

Figure 4

Motor activity of type I R-M Enzyme. (a) The yellow block represents the DNA-binding (recognition) site of the enzyme, which is represented by the green object approaching from the top of the diagram and about to dock onto the recognition sequence. (b) The motor is bound to the DNA at the recognition site and begins to attach to adjacent DNA sequences. (c) The motor begins to translocate the adjacent DNA sequences through the motor/DNA complex, which remains tightly bound to the recognition sequence. (d) Translocation produces an expanding loop of positively supercoiled DNA. The motor follows the helical thread of the DNA resulting in spinning of the DNA end (illustrated by the rotation of the yellow cube). (e) When translocation reaches the end of the linear DNA it stops, resets and then the process begins again.

Figure 5

Inverse temperature solubility behavior of responsive polymers at the Lower Critical Solution Temperature (LCST). Left hand side shows hydrated polymer below LCST with entropic loss of water and chain collapse above LCST (right hand side).

Figure 6

Schematic representation of the molecular motor function controlled by a thermoresponsive polymer switch. R, M and S denote the specific motor subunits. Chain-extension of the polymer below LCST provides a steric shield blocking the active site. Chain collapse (above LCST) enables access to the active site and restoration of enzyme function. For more details see text.