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Evaluating the Use of Spartan in Studying the Effects of Charged Lysine Residues

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Evaluating the Use of Spartan in Studying the Effects of Charged Lysine Residues Evaluating the Use of Spartan in Studying the Effects of Charged Lysine Residues Mark Lazari Abstract Spartan by Wavefunction, Inc. is a powerful computational modeling tool that is used in both the research and academic realms.1 This study reviews Spartan's ability to run conformational searches on alanine and lysine containing peptides, and compares Spartan's calculated values to those of Gaussian, another computational modeling program. The goal is to begin steps in understanding the effects of protonation of a lysine residue in a string of alanine residues, where lysine will reside either as the amino acid on the N-terminus or the C-terminus of the peptide. The study found that the protonation of a lysine residue placed at the C-terminus stabilized the α-helical structure of the peptide, and destabilization of the α-helix occurred when the protonated lysine residue was placed at the N-terminus. Spartan allows for a more user-friendly approach to conformational searches than Gaussian, and it gives a more graphical view of the conformations. This allows for better viewing of the structures and conformations while simultaneously calculating their thermodynamic data. Background statistical mechanics methods based on quantum mechanics. The details of these Introduction to Computational Chemistry theories and resulting mathematical methodologies will not be covered in this Computational Chemistry has revolutionized paper. For clarity, any mention of "methods" our way of viewing molecules at the quantum refers to the particular mathematical approach mechanical scale by allowing us to simulate taken to run a calculation. Examples of these various chemical scenarios that are not methods include but are not limited to semi- possible to study in a lab. In Organic empirical AM1, molecular mechanics or Chemistry, the transition states of molecules MMFF, and density functional B3LYP/6- represent the theoretical structure molecules 31G*). go through during a reaction. In lab, these As one might assume, something based transition states cannot be isolated. With solely on simulations from statistics and Computational Chemistry, the transition states probability has its advantages and can be modeled, and their thermodynamic disadvantages. Many of the advantages are properties can be studied in various listed above, however, the disadvantage is conditions (e.g. solvents, gas-phase, etc.) and clearly a lack of tangible, reproducible at various temperatures. For Biochemistry, experimental lab results. Many in silico proteins can be better understood in terms of studies are done in tandem with experimental their behavior with other molecules (e.g. an data, and many computational programs enzyme binding to its substrate), and the contain built-in protocols to help researchers structures and conformations of peptides and better compare experimental data with the nucleic acid sequences can be more readily calculated theoretical results. By comparing seen and understood via computational reproducible computational data with simulations. This in silico work draws its reproducible lab data, one can better fine-tune basis from what we have learned thus far the programming to continually gain more from Physics and Physical Chemistry by reliable results. bringing in wavefunction theory and various Spartan Review forms (e.g. ball and stick, tube, etc.), as well One program that is used for as reveal any hydrogen bonding, ribbons for computational analysis and molecular proteins, labels, chiral centers, etc. Using modeling is Spartan by Wavefunction, Inc. some keyboard shortcuts and keyboard-mouse Spartan boasts a more user-friendly interface combinations, the user can also rotate the in terms of modeling and programming, molecule at a which lowers the learning curve in both the chosen bond, academic and commercial realms of research. adjust the bond The modeling aspect is simple, length, and adjust straightforward, and allows for a wide range the chirality of of molecules to be built quickly and given chiral efficiently. Spartan separates modeling centers. For "pieces" in terms of their relative uses, as seen further in Figure 1 to the right, which is taken from customization, Spartan '08. One tab in Spartan's build menu the user can lock is set up specifically to deal with most organic certain bond molecule pieces, such as tetrahedral carbon lengths, angles, atoms, trigonal pyramidal nitrogen atoms, as and dihedral well as groups such as benzene rings and angles, and use carbonyl groups. Another tab allows for more those constraints customizability, which is used most often for as starting points Inorganic Chemistry. This tab gives the user as well as the ability to choose the atom, its geometry, limitations when and its bond type (i.e. single, double, triple, optimizing the etc.). Spartan's builder also allows for amino molecule's acids and nucleic acids to be added geometry. One individually or in sequence. For peptides, the example of this is forcing an ammonia (NH3) user has the option to give the amino acid molecule to remain in its trigonal planar sequence an α-helix or β-sheet conformation geometry, which represents the transition as well as choose how to terminate the state of ammonia during inversion. This can peptide at both the N-terminus and C- be seen in Figure 2 below. With these tools, terminus. Using the peptide builder in the user can effectively build a molecule, concert with the other builder tabs, the user view and adjust its restrictions and conditions, can easily adjust the peptide to fit his or her and label the molecule and its constituents for own personal needs. complete customizability all while having an easy to understand visual representation of Once the molecule is built, depending on these changes. the version of Spartan one has (e.g. '02, '06, '08), the user can view the molecule in various Spartan keeps is determined by the amount the user had defined to keep as well as the Spartan Calculations energy interval designated for the samples. After a molecule has been built, a series of By default, this interval is set to 40 kJ/mol, calculations can be done on it that will and only versions of Spartan '06 and above optimize it in terms of energy. Essentially, have the ability to adjust the default energy the calculations serve to find the lowest interval value. Spartan will search through energy conformation, or the arrangement of and calculate the energies of all the the atoms of a molecule in three-dimensional conformations allowed by the user (e.g. 5000 space. How Spartan does this is dependent on of the 200,000) using the defined method (e.g. the type of calculation desired, which are semi-empirical AM1) and generate in a explain below. Spartan will also calculate a separate file the number of conformations variety of chemical and physical properties defined by the user, assuming it was able to that are common for all molecular modeling find that many conformations within the programs. The advantage Spartan has over defined energy interval. If 100 conformations many other modeling programs, however, is are kept, Spartan will generate 100 the fact that it can calculate and output a conformations that are within an interval of molecule's conformations at various energies. energies that range from most energetically This is helpful in analyzing, understanding, favorable to 40 kJ/mol higher than the and determining the physical representations favorable energy (assuming the default energy of organic and biological molecules in both interval was used). Due to Spartan's graphical the energetically favorable (high energy) and nature, these conformations can be easily unfavorable (low energy) conformations. viewed and judged both in terms of structure The calculations used in this study are and energy. The amount of conformations the conformer distribution, equilibrium geometry, computer can search through and store are and energy (or single point energy). Spartan greatly limited by the computer's RAM offers other calculations for transition state capacity and available hard drive space. The analysis, other conformational search speed, aside from the computer's processor protocols, etc. that can be found in the quality, is determined by the method for program's handbook. These calculations are energy calculations set for each conformation used to quickly, efficiently, and accurately (e.g. semi-empirical, molecular mechanics, determine the most energetically favorable etc.). conformations of each polypeptide. The Equilibrium geometry is one of the more methods are explained in the following straightforward calculations to run using sections, but the follow are brief summaries Spartan, and its goal is to simply optimize the of what each calculation does. geometry of the molecule in terms of energy. Conformer distribution uses the Monte What makes Spartan a powerful program is its Carlo method of searching through possible ability to optimize a series of molecules conformations of molecules. The Monte stored within a given file. For example, if the Carlo method is described below. Spartan 100 conformations retained from the allows the user to customize the amount of conformer distribution calculation were conformations that will be searched through determined using molecular mechanics (e.g. a simple two residue peptide has on the calculations, and the user wanted to optimize order of 200,000 possible conformations) as each molecules' geometry in terms of AM1 well as tell Spartan to retain the structures of a calculations,
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