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This tutorial is about modeling the formation of protein complexes in complex environments. It starts by describing the process of protein folding, before moving on to how protein complexes are formed. The tutorial also addresses how different interactions between proteins can affect their stability and the possibility that proteins can aggregate into structures that have novel properties. Finally, it concludes with a section discussing some current research in this field. Protein folding plays a central role in biology as it determines the function of a protein. This process can be broadly divided into two main steps: folding of the polypeptide chain into an alpha-helix and then the packing of these helices to form a compact globular structure. Folding begins with the release of water molecules from between hydrophobic residues, which can be described as a glass-rubber transition. The formation of secondary structures such as beta-sheets and alpha-helices involves hydrogen bonds and salt bridges – these are interactions that fall under the umbrella of noncovalent interactions. In contrast, folding is mainly driven by enthalpic interactions, i.e. interactions between different parts of the same molecule. The formation of protein complexes also plays a key role in biological processes. Key examples include the formation of the nucleoprotein complex, the actin-binding proteins in the cytoskeleton, and the interaction between structural proteins in cell membranes. How different interactions between proteins can affect their stability and how these interactions can be used to alter the functionality of proteins are two other key research areas in this field. Finally, some current research in this field is focused on understanding how misfolded proteins can aggregate to form amyloids and prions. These amyloids have been implicated in a wide range of diseases including Alzheimer’s, Parkinson’s, and Huntington’s diseases. After DNA replication has been completed the cell faces the challenge of ensuring that all the new nucleic acids fold correctly into a functional protein. This process begins with a single molecule of mRNA that begins to fold into a three-dimensional structure. The mRNA molecule has a complex secondary structure containing intronic regions and exonic regions which have different functions. After the first round of mRNA folding, a protein called a ribosome can bind to the mRNA. Ribosomes are composed of RNA and protein and there are two different types: 5' and 3' type ribosomes. The function of these is to become active during the second round of mRNA folding. In this process there is a conformational change that brings together the various regions of the mRNA molecule into a conformation that allows it to fit into a functional RNA polymerase. This is an important step as incorrect folding of messages results in malfunctions in proteins. It has been shown that this conformational change can be affected by environmental factors such as exposure to light or stressors introduced by external agents such as chemicals or toxins. cfa1e77820
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