Proteins formed by a long chain of

Proteins are one of the most sophisticatedmolecules structure known today. They are formed by a long chain of organic componentsknown as amino acids. Proteins functions as the essential building blocks toliving organism by providing the ability to replicate DNA chains, catalyzemetabolic reactions, transport molecules from one location to another and manymore. To perform these complex functions, proteins need to first folds its chainof amino acids into a three-dimensional structure in a process called proteinfolding. Our current understanding is that folding happens spontaneously drivenby the effects of hydrophobic entropy changes and the interactions with molecularchaperones. (Alberts, 2002) The hydrophobic effect is often consideredthe main driven force behind protein folding.  Before the folding process began, the proteinis still in the form of amino acid chain.

The chain consists of manyhydrocarbon based amino acid such as alanine, leucine and tryptophan. Onecrucial property of hydrocarbons is that they behave hydrophobically like oiland fat. The chain then spontaneously folds into its core due to thehydrophobic effects. The folding process completes when the surrounding watermolecules and the oil-like amino acid chains stabilize into an equilibrantstate. While forming hydrogen bonds within the protein do create a strongstructure, much of the transformation is due to minimizing the number ofhydrophobic chains exposed to surrounding water molecules (Rose, 2006). Finally, water molecules forman intricate cage around the newly developed protein which increase the entropyby creating order. As the entropy increases, protein transformed into itsfolded structure.

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Clearly, this folding process follows the second law of thermodynamics. Molecular chaperones also take an important role in theprocess of protein folding. While they are not required for most of the protein’sfunction, intramolecular chaperones are essential for the folding process (Hendrick, 1995).

The type I molecular chaperones assist amino acids to foldinto their three-dimensional structures by producing N-terminal sequenceextension. The type II molecular chaperones mediate the formation of structurewith C-terminal sequence extension. Chaperones interact with newly formed chainwhich prevent their premature collapse until stable structure is synthesized. Whenproteins failed to fold into its correct form, molecularchaperones will bond with the hydrophobic amino acids that are exposed to theenvironment. Then they will help proteins returning to desired state byinducing a heat shock. While heat shock protein (HSP) chaperones are the mostcommonly seen ones, there are also other type of molecular chaperones that usesdifferent mechanism to achieve the similar folding assisting effects.

 The recent discoveries in theprocess of protein folding created a very important field of research calledcomputational protein structure prediction (Levitt,1975). We are now able to simulate the driving force of protein foldingwith powerful computers in a virtual environment. One noticeable project [email protected] created by Stanford University uses the idle resources from hundredsof thousands of personal computer and gaming console to simulate the proteinfolding process. With a computing power of over 130 petaflops, it is ranked oneof the fastest computing systems in the world. Another research direction withgreat potential is analyzing protein folding with Deep Learning (Wan, 2016). Theamount of information in each amino acid chain is well beyond of currentcomputing ability. With the algorithm presented by Wan et al.

we canpotentially exploit the complex latentfeatures within each amino chain using deep neural networks. The advancement ofmachine learning and self-improving intelligent algorithms will certainly be animportant step for protein folding research. ­­­­­In conclusion, protein foldingis driving primarily by the hydrophobic effects in which the chain of amino acids collapsed inwardforming three-dimensional structure. Protein folding is also assisted byfurther stabilized by the binding of molecular chaperones. The entire processof protein folding happens spontaneously and is entropy positive. Based onthese observations we have developed a system of computer based simulation toassist the research of the protein structures.

Understanding the cause and effectof protein folding is vital to our exploration into the origin and developmentof life. We hope these researches will give us the key insights to thetreatment of currently incurable diseases and open ways for designing drugswith highly efficient computational techniques.  

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