Studying Sequence-Structure Relationships Of Proteins By Molecular Dynamics Simulation

Proteins are the main executors of biological functions,participating in almost all biological activities.Although it is well-known that DNAs are transcribed into mRNAs,then mRNA translated to proteins,our understanding about how amino acid sequences encode protein structures and functions is still limited.Examples inlcude how the subtle differences in sequences between proteins of the same family or between different mutants of a protein may affect stability of proteins in solution,change the conformational free energies,influence the oligomerization states,modulate the protein-ligand and protein-protein interactions,and so on.For now,these questions need to be studied case by case.The analysis of specific cases not only facilitates deeper understanding of the structure and biological functions of particular protein families,but also accumulates instances for understanding the subtler and precise relations between sequence-structure and function.Such understaning may also help to improve the success rate of protein design.Molecular dynamics simulation is an important method for studying protein sequence-structure-function relationships.In the current thesis,I use molecular dynamics simulations to specifically discuss the relationship between the functional differentiations of proteins in the abscisic acid receptor family and their differences in sequences and structures(Chapter 2).Through comparative analysis,I confirmed that the stability of monomers,homodimers and receptor-phosphatase heterodimers of different abscisic acid receptor subfamilies have different dependences on the existence of abscisic acid.Some sequence differences between subfamilies may be responsible for the differentiations in structural stability,and further for those in functional differences.The results of free energy calculations(Chapter 3)also support the different constitutive inhibition levels of different receptor subfamilies on downstram phosphatase.Protein design can also facilitate deeper understanding of protein sequence-structure relationships.On the other hand,the design of proteins with specific structures and functions has high potential application value.Molecular dynamocs simulation can be applied to the optimization,screening of computational protein design and also can give feedbacks.In the fourth chapter,we use molecular dynamics simulations to explore the possible molecular mechanisms of the improvement of a designed protein through directed evolution,and discuss the effects of each mutation site on the stability of the designed protein.In Chapter 5,we explored molecular dynamics simulations to improve the anti-cavitation properties of two designed proteins.Using molecular dynamics simulation combined with spatial aggregation propensity scoring function,we determined the possible key sites affecting the solubility of these two designed proteins,then we carried out the corresponding mutations and obtained improved proteins.