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Constructing globular, sheeted and helical polyalanine structures using nanotubes as templates for computational studies.

Article Excerpt
ABSTRACT

In this experiment polyalanine was folded into globular, sheeted and helical structures through the use of carbon nanotubes. The rigidity of the nanotubes allowed for molding the polyalanine into the various structures. Nanotubes of different diameters and volumes were used in this experiment. Once the three dimensional peptide structures were formed and detached from the carbon nanotubes, a number of thermodynamic calculations were performed. Computational methods were used to calculate parameters such as Gibbs free energy, enthalpy, entropy, and molecular volume. By attaining the measurements of the [PHI] and [PSI] angles, Ramachandran plots were constructed using linear, globular, sheeted and helical protein structures.

INTRODUCTION

i. Protein Structure

Proteins serve many biological functions in the body such as [O.sub.2] transporters and building up immunity against infection or disease. The functions of proteins are dictated by their structure or conformation. There are twenty well known amino acids that are classified into five categories: nonpolar, aliphatic R groups: (i.e. glycine, alanine); aromatic R groups: (i.e phenylalanine); polar, uncharged R groups: (i.e. serine, asparagines); positively charged R groups: (i.e. lysine); and negatively charged R groups: (i.e. aspartate). Alanine (see Figure 1) and peptides of polyalanine are the focus of this study.

Proteins are made of amino acids joined covalently by peptide bonds. The peptide bonds are formed through condensation reactions in which a water molecule is lost. Proteins are long polypeptide chains ranging from one hundred to several thousand amino acid residues and can adapt to different geometries. The backbone of the polypeptide chain is composed of the alpha carbon ([C.sub.a]) which is linked to the carbonyl carbon. The carbonyl carbon is bonded to the nitrogen forming the backbone (see Figure 2).

[FIGURE 1 OMITTED]

[FIGURE 2 OMITTED]

If the carbon-nitrogen bond has double bond characteristics, it cannot rotate freely. The bonds between the carbonyl carbon and the alpha carbon and between the nitrogen and the alpha carbon are the only bonds in the backbone that can move freely. If a large side chain is attached then the movement of the backbone will be stericly inhibited. Since the carbonyl carbon and nitrogen bond are fixed, it is possible to calculate the angles made between two nitrogen atoms ([PHI]) or two carbonyl carbons ([PSI]) relative to the plane of the carbonyl carbon-nitrogen bond. Since the bond angles can range from -180 to +180, there are a number of conformations a protein can undergo.

There are four levels of protein structures. These structures. These include primary, secondary, tertiary, and quaternary structures. The primary structure is the order or sequence of linear chains of amino acids present. The secondary structure is a local region of organized structure and...

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