Molecular Dynamics Simulation Studies Of The Fold And Stability Of Collagen-Like Peptides

Collagen is abundant in the human body.Despite the structural and functional diversity of distinct types of collagens,they all share a common characteristic structure,the triple helix.The GXY repeat is the characteristic motif of the triple helix amino acid sequence,where G is Gly.X and Y position can be occupied by any amino acids such as Pro.Understanding the relationship between the amino acid sequence and the stability of triple helix structure is the foundation for comprehending the structure and function of collagen,however,the physical and chemical mechanism is not clear.Based on the sequence of collagen heterotrimer ABC,this study established both triple helix and single chain host-guest peptide system.By using a combination of molecular dynamic simulation and biophysical experiments,the influence of salt bridges formed between different amino acids on the thermal stability of collagen triple helix was analyzed.In addition,the effect of different amino acids on the pre-organization of single chains was analysed by molecular dynamic simulation.This work will aid in the comprehension of the stability mechanism of the triple helix structure of collagen’s amino acid sequence and provide a reference for the design of novel collagen heterotrimers.This reaserach mainly contains sveral aspects as below:(1)On the basis of the positive-negative charge pattern of the heterotrimer ABC,forty-eight heterotrimers which contained 16 types of salt bridges were synthesized.The thermal stability(T_m)was characterized by circular dichroism.Results show that the energetic contribution(ΔT_m)of salt bridges should be additive to the triple helix structure.Three crystals of the heterotrimers were solved by X-ray,followed by a molecular dynamic simulation.The same salt bridge type has similar side chain conformation.Strong salt bridges have shorter salt bridge distances and more stable interactions,while weak salt bridges have longer salt bridge distances and more scattered side chain dynamics.The T_m of 48 heterotrimers were fitted by theΔT_m of 16 types of salt bridges with a high correlation(R~2=0.93).The results showed that the thermal stability of heterotrimers could be predicted by the contribution of salt bridges.(2)On the basis of the single chains(Chain C and B)of the heterotrimeric ABC,17 amino acids were introduced into the X and Y position,respectively.A total of 2×18=36 collagen-like polypeptide single-chain models were designed.The backbone dynamics of the mutation aimino acid and its adjacent amino acid were characterized by molecular dynamic simulation.Results show that all chains are disordered.Different amino acids show specific preference of backbone conformation,which also affects the conformation of the adjacent amino acid.The polyproline II type(PPII)propensity of most amino acids showed a high correlation with the triple helix propensity.Pro had the highest occupancy of forming the PPII conformation at the X position.Similarly,hydroxyproline(Hyp)had the highest occupancy at the Y position,indicating that the properties of these amino acids pre-organized into PPII structures in collagen folding precursors may be related to their tendency to form triple helix structures.