Proteins are one of the most sophisticated molecules structure

Proteins are one of the most sophisticated
molecules structure known today. They are formed by a long chain of organic components
known as amino acids. Proteins functions as the essential building blocks to
living organism by providing the ability to replicate DNA chains, catalyze
metabolic reactions, transport molecules from one location to another and many
more. To perform these complex functions, proteins need to first folds its chain
of amino acids into a three-dimensional structure in a process called protein
folding. Our current understanding is that folding happens spontaneously driven
by the effects of hydrophobic entropy changes and the interactions with molecular
chaperones. (Alberts, 2002)


The hydrophobic effect is often considered
the main driven force behind protein folding.  Before the folding process began, the protein
is still in the form of amino acid chain. The chain consists of many
hydrocarbon based amino acid such as alanine, leucine and tryptophan. One
crucial property of hydrocarbons is that they behave hydrophobically like oil
and fat. The chain then spontaneously folds into its core due to the
hydrophobic effects. The folding process completes when the surrounding water
molecules and the oil-like amino acid chains stabilize into an equilibrant
state. While forming hydrogen bonds within the protein do create a strong
structure, much of the transformation is due to minimizing the number of
hydrophobic chains exposed to surrounding water molecules (Rose, 2006). Finally, water molecules form
an intricate cage around the newly developed protein which increase the entropy
by creating order. As the entropy increases, protein transformed into its
folded structure. Clearly, this folding process follows the second law of thermodynamics.

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Molecular chaperones also take an important role in the
process of protein folding. While they are not required for most of the protein’s
function, intramolecular chaperones are essential for the folding process (Hendrick, 1995). The type I molecular chaperones assist amino acids to fold
into their three-dimensional structures by producing N-terminal sequence
extension. The type II molecular chaperones mediate the formation of structure
with C-terminal sequence extension. Chaperones interact with newly formed chain
which prevent their premature collapse until stable structure is synthesized. When
proteins failed to fold into its correct form, molecular
chaperones will bond with the hydrophobic amino acids that are exposed to the
environment. Then they will help proteins returning to desired state by
inducing a heat shock. While heat shock protein (HSP) chaperones are the most
commonly seen ones, there are also other type of molecular chaperones that uses
different mechanism to achieve the similar folding assisting effects.


The recent discoveries in the
process of protein folding created a very important field of research called
computational protein structure prediction (Levitt,
1975). We are now able to simulate the driving force of protein folding
with powerful computers in a virtual environment. One noticeable project called
[email protected] created by Stanford University uses the idle resources from hundreds
of thousands of personal computer and gaming console to simulate the protein
folding process. With a computing power of over 130 petaflops, it is ranked one
of the fastest computing systems in the world. Another research direction with
great potential is analyzing protein folding with Deep Learning (Wan, 2016). The
amount of information in each amino acid chain is well beyond of current
computing ability. With the algorithm presented by Wan et al. we can
potentially exploit the complex latent
features within each amino chain using deep neural networks. The advancement of
machine learning and self-improving intelligent algorithms will certainly be an
important step for protein folding research.


­­­­­In conclusion, protein folding
is driving primarily by the hydrophobic effects in which the chain of amino acids collapsed inward
forming three-dimensional structure. Protein folding is also assisted by
further stabilized by the binding of molecular chaperones. The entire process
of protein folding happens spontaneously and is entropy positive. Based on
these observations we have developed a system of computer based simulation to
assist the research of the protein structures. Understanding the cause and effect
of protein folding is vital to our exploration into the origin and development
of life. We hope these researches will give us the key insights to the
treatment of currently incurable diseases and open ways for designing drugs
with highly efficient computational techniques.