Theory And Simulation Of Biomacromolecules

Biopolymers, which have the complicated and compact conformations to embody their biological function, are a physical foundation of the life. Biopolymers include protein, nucleic acid, polysaccharide and lipid. These biopolymers need the specific three-dimensional structure to play their functions. In this dissertation, our main purpose is to uncover the structure property of proteins, DNA and polysaccharide gel. It's important to study the folded conformations and folding mechanism that is the key point to understand the biology.In Chapter 2, we have investigated statistical properties of contacts based on two models, which called coarse model and each atom counted model. By analyzing the effects of amino acid residue on long- and short-range contacts in coarse model, we can conclude that hydrophobic residues, such as Leu, Val, Ile, Met, Phe, Tyr, Cys, and Trp are easy to form long-range contacts, while hydrophilic residues, such as Glu, Gln, Asp, Asn, Lys, Ser, Arg, and Pro are difficult to form long-range contacts. Long-range contacts contribute more functions to protein folding and play an active role in the stability of proteins. However, the ability to form short-range contacts only depends on the protein sequence. Statistical properties of contacts in globular proteins are also studied. The results show us that different globular proteins have different ability to form contacts, i.e., all-αproteins are difficult to form sequential long-range contacts, while all-βproteins are easy to form it, which strongly depended on their secondary structure. Considering different side group structure and interaction between each atom in a residue, new atom pair contacts are introduced in the each atom counted model. In this model, the ability to form long-range atom pair contacts can be well described by the hydrophobicity scale of the residue in detail. Therefore, it's more effective to characterize the conformation of proteins, especially in protein folding rate prediction. There is the relationship between the protein folding rateΚfand the contact order (CO), total contact distance (TCD) and long-range order (LRO). Comparing these three parameters, TCD is more effective to predicting folding rate and a relationship is lnKf= -13.2×TCD+19.73. The new prediction method by BP neural network model is also investigated here and more accurate result is obtained. In this model that CO, LRO and TCD are treated as input nodes to predicte protein folding rate is more effective than TCD. It is concluded that the folded structure of a protein depends on CO, LRO and TCD simultaneously. These results can help us to understand the property of protein structure and its mechanism of folding well.In Chapter 3, the relationship between the conformation and energy of DNA is studied under the elastic rod model by Metropolis Monte Carlo simulation firstly. The bending energy EB is about 10 - 102 times larger than twisting energy ET. The relationship between the mean square distance R2g and chain length is also found. Second, the new two-dimensional walk model of DNA, with considering a pair of sequential nucleotides is introduced here. Some linear correlations are obtained in the double logarithmic plots of mean square distance< R2 (l)> and fluctuation F(l) versus nucleotide distance l along DNA chains. In the study of power spectrums, the difference between coding and no-coding DNA sequence is that there is a notable peak value occurs at 3.33×10-1bp-1 in coding DNA sequence. Finally, the Hamilton actuating quantity considering the bending and stretching elastic potential energy is calculated to investigate the dynamic property of polymers. The dependence of the relaxation time on the persistence length is also discussed here. In the flexible limit, the expression of the relaxation timeτn is the same as one in the Rouse mode, i.e.τn∝L2n-2. In the stiff-chain case, such as DNA chains, the expression of the relaxation time isτn∝[L/(2n-1)]4. These analyses include the primary structure (DNA sequence), tertiary structure (DNA conformation) and the dynamic property of DNA, which help us to obtain more detailed information on DNA.In Chapter 4, the frictional behavior of different counterions gellan gel against a glass plate is investigated. Gellan gel is one of the polysaccharide gels, which are widely used in the food industry. The low friction coefficients are observed on either Na+-gellan or Ca2+ -gellan gel measured in pure water or high concentration salt solution, especially the samples rotated under the low angular velocity. It's the advantage as artificial cartilage materials. The fictional behavior of different counterion gellan gel is not same because of different formation type of double-helical junction-zones, followed by aggregation of the double-helical segments. On the other hand, the frictional stresses of gellan gels are increasing with the increase of immersion time. The observed specific phenomenon seems to be originated from the instability of the network of gellan gel. These results are useful to utilize its full potential as a functional ingredient for foods and biotechnology materials.