Narrow Results

We discuss the approach to investigate molecular machines using systems of integro–differential ultrametric (p-adic) reaction–diffusion equations with drift. This approach combines the features of continuous and discrete dynamic models. We apply this model to investigation of actomyosin molecular motor.

The introduced system of equations is solved analytically using p-adic wavelet theory. We find explicit stationary solutions and behavior in the relaxation regime.

Catenanes and rotaxanes containing porphyrin subunits have become popular synthetic targets because of the large variety of available synthetic strategies including the coordination chemistry of metalated porphyrins, coupled with the many attractive physical properties of porphyrins. The present review article outlines various synthetic approaches and templating strategies that have been used to prepare a range of mechanically interlocked architectures that incorporate porphyrins as fundamental subunits either grafted onto macrocycles or as stoppers. These species are of interest in relation to recreating natural processes such as the photosynthetic apparatus or enzyme binding sites. In recent years, "molecular machines" have also experienced a spectacular development. Porphyrin-based rotaxanes are particularly promising in relation to this research field, this is shown by the elaboration of a "molecular press" whose properties will be briefly discussed in this review.

Movement and shape changes are fundamental aspects of all living organisms. This biological motility results from the biological nanomotors, in particular protein nanomotors. Cells contain a variety of protein nanomotors that rotate (e.g., F₀F₁-ATP synthase or bacterial flagellar motors) or move in a linear fashion (e.g., the kinesin, myosin and dynein motors). F₀F₁-ATP synthase is one of the ideal nanomotors or energy providing systems for micro/nanomachines because of its small size, smart and perfect structure, and ultra-high energy transfer efficiency. Therefore, in this paper, we have reviewed the structure, mechanism, and potential applications of the F₀F₁-ATP synthase nanomotor. In all organisms, the F₀F₁-ATP synthase consists of two distinct nanomotors, F₀ and F₁. The F₀ moiety is embedded in the membrane and is a detergent soluble unit while the F₁ moiety protrudes from the membrane and is a water soluble unit. F₀F₁-ATP synthase operates as two stepper motor/generators coupled by a common shaft and an electrochemical-to-mechanical-to-chemical energy transducer with an astounding 360° rotary motion of subunits. F₀F₁-ATP synthase nanomotor may enable the creation of a new class of sensors, mechanical force transducers, actuators, and nanomechanical devices. Thus, the F₀F₁-ATP synthase nanomotor field has expanded into a wide variety of science.

Supramolecular chemistry is the chemistry of “designed noncovalent intermolecular interactions”. In this chapter we will trace the beginnings of supramolecular chemistry from molecular recognition through the more recent advances in the design of prototypical molecular machines.

Even though its structure is known to atomic resolution, the ways in which the ribosome accomplishes its tasks in synthesizing proteins are still unknown. The key to an understanding of its dynamics might be found in cryo-electron microscopy of trapped states, and an interpretation of the resultant density maps by “molding” the X-ray structures into them. First results, obtained by application of real-space refinement techniques to cryo-EM maps of complexes in different conformations, indicate a complicated internal reorganization. The question arises as to whether the observed conformational changes accompanying ribosomal function might be predictable based on the architecture of the macromolecular complex. It has indeed been possible to derive one of the principal motions (the ratchet motion) by normal mode analysis of the ribosome represented as a simplified mechanical system.

Mass spectrometry is an analytical technique which, as its name implies, “weighs” molecules, and thereby can define molecular identity, interactions and reactions. With this technique, molecules from a source are ionized (i.e. made to carry a formal charge, either negative or positive) and subsequently enter the mass analyzer where ions are separated according to their mass/charge ratio (m/z), and then a spectrum is recorded as ions reach the detector. Initially applications were limited to small molecules but nowadays even large macromolecular complexes are amenable for analysis.