MOLECULAR MACHINES fundamentals




Molecular machines are tiny energy conversion devices on the molecular-size scale. Whether naturally occurring or synthetic, these machines are generally more efficient than their macroscale counterparts. They have their own mechanochemistry, dynamics, workspace, and usability and are composed of nature’s building blocks: namely proteins, DNA, and other compounds, built atom by atom. With modern scientific capabilities it has become possible to create synthetic molecular devices and interface them with each other. Countless such machines exist in nature, and it is possible to build artificial ones by mimicking nature. Here we review some of the known molecular machines, their structures, features, and characteristics. We also look at certain devices in their early development stages, as well as their future applications and challenges.

Molecular machines can be defined as devices that can produce useful work through the interaction of individual molecules at the molecular scale of length. A convenient unit of measurement at the molecular scale would be a nanometer. Hence, molecular machines also fall into the category of nanomachines. Molecular machines depend on inter- and intramolecular interactions for their function. These interactions include forces such as the ionic and Van der Waal’s forces and are a function of the geometry of the individual molecules. The interaction between two given molecules can be well understood by a set of laws governing them, which brings in a definite level of predictability and controllability of the underlying mechanics. Mother Nature has her own set of molecular machines that have been working for centuries and have become optimized for performance and design over the ages. As our knowledge and understanding of these numerous machines continues to increase, we now see a possibility of using the natural machines, or creating synthetic ones from scratch, by mimicking nature. In this review, we try to understand the principles, theory, and utility of the known molecular machines and look into the design and control issues for creation and modification of such machines. A majority of natural molecular machines are protein based, whereas the DNA-based molecular machines are mostly synthetic. Nature deploys proteins to perform various cellular tasks, from moving cargo to catalyzing reactions, whereas DNA has been retained as an information carrier. Hence, it is understandable that most of the natural machinery is built from proteins. With the powerful crystallographic techniques now available, protein structures are clearer than ever. The ever-increasing computing power makes it possible to dynamically model protein folding processes and predict the conformations and structure of lesser known proteins. These findings help unravel the mysteries associated with the molecular machinery and pave the way for the production and application of these miniature machines in various fields, including medicine, space exploration, electronics and military. We divide the molecular machines into three broad categories—protein based, DNA-based, and chemical molecular motors. ATP-BASED PROTEIN MOLECULAR MACHINES Three naturally existing rotary motors have been identified and studied in detail so far. Two form the F0F1-ATP synthase, and the third one is the bacterial flagellar motor. The protein-based molecular motors rely on an energy-rich molecule known as adenosine triphosphate (ATP), which is basically a nucleotide having three phosphate molecules that play a vital role in its energetics, and make it an indispensable commodity of life. The machines described in this section, the F0-F1 ATPase, the kinesin, myosin, and dynein superfamily of protein molecular machines, and bacteria flagellar motors all depend, directly or indirectly, on ATP for their input energy. These machines, which have been carrying out vital life

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