Computational studies on conformations and properties of peptide and amino acid nanobiomolecular complexes


Student thesis: Doctoral Thesis

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  • Cuihong WANG


Awarding Institution
Award date16 Jul 2012


Amino acids and peptides are the building blocks of proteins and biomolecules. Theoretical researches about the structures and properties of the former are important for understanding the latter. In this thesis, we performed systematic researches on the structures and properties of dipeptide arginylglycine and tetrapeptide phenylalanine-glycine-glycine-valine, and explored the possibilities to identify amino acids using carbon nanotubes and to design cage-like molecules formed by amino acids for drug delivery. In chapter 1, we introduce the basic theories of quantum chemistry calculations and several computational methods, such as Hartree-Fock theory, semi-empirical methods, perturbation theory, configuration interaction and coupled cluster methods. We also introduce the density functional theory, Atoms in Molecules, theory of molecular orbital and density of states. Finally, the simulation packages (Gaussian and DFTB+) we used in this work are briefly introduced. In chapter 2, the structures and properties of the neutral, protonated, deprotonated and metal cationized dipeptide arginylglycine were comprehensively studied. For clarity, we present the results in three parts. In part one, the canonical and zwitterionic conformers of dipeptide arginylglycine were thoroughly researched and we found that the most stable conformer has a zwitterionic structure. Zwitterions play important roles in the structure and function of peptides and proteins; however, the zwitterionic structures are not stable in the gas phase. Therefore, the arginylglycine appears to be the smallest peptide with stable zwitterions. The properties of the low energy conformers of the arginylglycine were systematically revealed, including the rotational constants, dipole moments and vertical ionization energies. In part two, the protonated and deprotonated conformers of the dipeptide arginylglycine (ArgGly±H+) were thoroughly searched. We obtained the thermochemical parameters, such as the proton affinity (PA), gas-phase basicity (GB), proton dissociation energy (PDE) and gas-phase acidity (GA). These thermochemical parameters are of fundamental importance for the interpretation of the molecules’ reactivity. The coordination of metal ions can significantly influence the intramolecular hydrogen bonds and electrostatic interactions of molecules. Thus, there has been increasing interest in understanding the effects of metal chelation on the structure of amino acids and peptides. In part three, we thoroughly researched the Na+, Rb+ and Mg2+ coordinated dipeptide arginylglycine (ArgGly). Our results show that the salt-bridge (SB) form is more stable for the sodium-cationized and rubidium-cationized dipeptides, but the charge-solvated (CS) form is more stable for magnesium-cationized dipeptide. The metal ion affinities (MIA) were researched too, which are found to be 69.0kcal/mol, 43.9kcal/mol and 283.8kcal/mol for complexes ArgGly·Na+, ArgGly·Rb+ and ArgGly·Mg2+, respectively. Finally, the IR spectra and the AIM electronic densities were calculated, and our results show that there are coexistence of red shift, blue shift and dihydrogen bond in the neutral, protonated and deprotonated dipeptide. The IR spectra of the metal ion cationized complexes shows that the same types of monovalent metal ion (Na+ and Rb+) coordinated complexes have similar spectra, but the spectra of divalent metal ion (Mg2+) coordinated complexes are quite different. The conformational distributions of all the complexes at various temperatures were investigated, which are expected to be helpful for experimental researches. Because the function of biological molecules is basically determined by the structure of the molecules, the structural research about the peptides and proteins is very helpful for knowing their functions. For most biological molecules, the aqueous solution phase is their natural environment. Although the structures of the molecules in solution are usually different from those in the gas phase, the research of the molecules in the gas phase can still uncover the intrinsic properties of molecules and shed light on the properties of the molecules in the natural environment at certain extent. As the knowledge of the conformation of small peptides will help to predict the structures of larger molecules and proteins, there have been many theoretical and experimental researches about them. In chapter 3, we thoroughly researched the neutral conformers of tetrapeptide phenylalanine-glycine-glycine-valine (FGGV) and found that most of the stable conformers have syn-carboxyl structures. Because of the difference of the backbones, the stable conformers can be divided into 13 groups and a γ-turn structure is the most favorite form. The relative energies, dipole moments and conformational distributions at various temperatures of peptide FGGV were analyzed. The IR spectrum calculation of the FGGV is expected to be helpful for understanding experiments. We also compared the structures of FGGV with the other tetrapeptides (GGGG, GVGG and GFGG), and found that the important conformers of these tetrapeptides have the same backbone structures. The experience received and the trends revealed can be used for further researches about the peptides, which is expected to reduce the number of the initial trial conformers, and then effectively reduce the computational costs. Identification and detection of different amino acid molecules as well as biological molecules have important scientific and technological significance. As an ideal one-dimensional nanomaterial, carbon nanotube (CNT) has various novel properties, valuable for both nanoscience and nanotechnology. The biomolecules can be adsorbed on the surface of carbon nanotubes by weak interactions, and the functional molecules can wrap around the nanotubes without losing their activity. Therefore, the functional molecules can be selected using the CNTs, as the different adsorbed complexes have different binding energies. In chapter 4, we investigated the adsorptions of three aromatic amino acids (phenylalanine, tyrosine, and tryptophan) on the sidewalls of a number of representative single-walled carbon nanotubes (SWNTs) using a density-functional tight-binding method, complemented by an empirical dispersion correction. The armchair (n, n) SWNTs (n=3-12) and zigzag (n, 0) SWNTs (n=4-12) were thoroughly examined. We found that the most stable amino acid/SWNT complexes for different SWNTs have similar local structures, and that the distance between the amino acid and SWNT is about 3 Å. Owing to the π-π and H-π stacking interactions, the benzene and indole rings in the amino acids are not exactly parallel to the SWNTs but instead lie at a small angle. We also investigated the diameter and chirality dependences of binding energies and found that SWNT (5, 0) has an especially large binding energy. We believe that the research about the interactions between the aromatic amino acids and CNTs will be helpful for the understanding of the interactions between large biomolecules and CNTs. And, the amino acids can be identified by the different binding energies. As the building blocks of proteins and components to build biological materials, amino acids and peptides are attracting increasing interest in scientific researches. The surrounded drugs by biological materials have specific controlled, sustained and targeted release characteristics, and the nanoscale drug delivery system can increase the parent drug solubility and maintain the structural integrity of the drug. In chapter 5, we selected the serine, one of the 20 natural amino acids, to be researched. The possible cage-like molecules formed by serine octamer or decamer were studied by calculations using the density functional tight-binding method, complemented by the empirical London dispersion energy term. Chirality is the essential concepts in chemistry and biology; it plays an important role for living organisms and has become a major concern in drug design. Thus, both the L-handed and D-handed serines were used to construct the complex conformers. The cage-like molecules were linked by the hydrogen bonds. The structures linked by -COOH...O=C- were found to be the most stable conformers, as evaluated by binding energies calculations and molecular dynamic simulations. The cage-like molecules have symmetric structures. The relative energies, binding energies and vibrational modes of the complexes were calculated and analyzed. In order to test the possible applications of the cage-like structures, we put the smallest fullerene C20 into the serine decamer. After optimization, we found that the amino acids-C20 complexes are very stable, which means that the cage-like structures might be useful to deliver small molecules. We expect that our results will be helpful for designing supermolecules for nanoscale drug applications. Chapter 6 will be a summary of the whole thesis work.

    Research areas

  • Peptides, Amino acids, Complex compounds