Proteins: From Bench to Bedside

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Central Dogma of Molecular Biology

“Life is a DNA software system” stated Craig Venter, who brought synthetic DNA into life. However, the proteins, which come in different forms and shapes, execute the functions of life. And, the molecule in between DNA and protein is RNA. In general, DNA could be replicated to another copy of DNA or transcripted to RNA, whereas, protein is translated from RNA. Occasionally, DNA could be reverse-transcripted from RNA, but protein can’t be reversed to RNA or DNA. This is the Central Dogma of Molecular Biology and is executed by different types of proteins.

Protein: The Workhorse of Life

Proteins are the ‘workhorse’ molecules of life. They are involved in every function of cells, including binding, catalysis, switching and providing structural support. Examples of binding include small ligand like oxygen binding to hemoglobin or binding of large DNA segment involved in transcription. Mostly enzymes are involved in biochemical catalysis, ranging from the production of energy from glucose by glycolytic enzymes to DNA replication by DNA polymerase. Switching in proteins is very crucial in signal transductions, which control many cellular functions. One such example is small GTPases, which are active in GTP bound forms, whereas inactive in GDP bound states. Structural proteins are extremely crucial for living organisms as these proteins provide them structural support. One common example is collagen in skin. This group of proteins is important source of biomaterials as well.

Protein Structure

Structure determines the function of a protein, and therefore, it’s important to determine the structure of a protein to understand the basic mechanism of action of the protein as well as to design and develop structure guided drugs. There are several methods to get 3D structure of proteins. Among these, X-ray crystallography and Nuclear Magnetic Resonance (NMR) are used extensively. Cryo-electron microscopy is also used for the determination of structures. Further, modeling of protein structure, based on the structure of a similar protein is also used. There are four levels of structure: primary, secondary, tertiary and quaternary. Primary structure is the sequence of polypeptide chain, a polymer of amino acids, which is decoded from the DNA sequence. These amino acids have an amine group and a carboxylic acid group connected to a central carbon atom. Four valencies of the central carbon is then satisfied by a hydrogen atom and one form another group of twenty side chains with varied structure and chemistry, starting with the simplest atom, hydrogen. This chain then folds into different forms like helix, sheet and turns, whereas, some regions are not folded and these flexible regions add versatility to the structures as well as functions. Hydrogen bonds formed between CO and NH from the main chain are mainly responsible for holding these forms, whereas, side chains  would determine what type of form it would adopt. These are termed as secondary structural elements. These elements of the whole chain then rearrange themselves to give tertiary structure. Two or more tertiary structural units can combine to give a quaternary structure, which has a high level of sophistication in terms of function.

Proteins are Flexible Molecules

Proteins are polymers of amino acids, linked by a single covalent bond, and, therefore, can rotate around this single bond, although certain portion, peptide plain, loses this flexibility because of partial double bond character. This flexibility helps the polypeptide chain to fold into different conformations depending on the environment and they are dynamic in nature. This dynamic nature of protein is absolutely essential for its function. If an enzyme has to work efficiently, it has to first bind its substrate(s), convert it to product(s) and then the product(s) should be released so that the enzyme can participate in the next round of reactions. One of the abundantly available proteins is serum albumin, which carries many substances, including drugs, in our body and delivers at the site of requirement. Flexibility in this protein renders it to be able to carry diverse compounds in physiological conditions.

The Structural Basis of Protein Functions

Structure-function relationship is one of the most interesting topics in protein chemistry. This could be approached in two different ways. Firstly, when the function of a protein is known, determining the structure could greatly help to understand the mechanism how the protein functions. On the other hand, if the structure is known, but not the function, then the function could also be predicted.

Proteins as Drugs and Drug Targets

Some proteins could be used as drugs whereas some could be targeted by drugs. Deficiency of insulin, which regulates blood sugar level, could lead to diabetes.  To treat this disease, insulin is injected directly in the blood as a drug. There are many examples of such drugs. Functions of proteins could also be blocked or enhanced using drugs. This blocking strategy has successfully been used in many diseased conditions, from microbial infection to cancer treatment. On the other hand, some drugs enhance the activity of proteins. One such example is Riociguat (trade name Adempas), used for the treatment of pulmonary arterial hypertension.  However, these have to be precise. Otherwise, some of the proteins of our body would start malfunctioning leading to side effects.

Proteins mediate life processes in a precise and varied way. Knowledge generated by decades of research on structure-function relationships in proteins could lead to the discovery and development of protein based materials to solve a vast array of problems. It would be possible to design proteins to perform customized functions using protein engineering in future to address many important challenges faced by our society.

Author: Dr Biswajit Pal, Senior Scientist, CSIR-Centre for Cellular and Molecular Biology.

Email: pal@ccmb.res.in

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