Edward J. Barrett

2 – COMPONENTS OF THE SYSTEM

This chapter presents the framework pieces used for polypeptide model construction and highlights the atomic framework pieces available and their structural uses. It describes the fused framework system pieces and atomic framework system with its use. Both the atomic and fused framework units can be modified to show the space-filling character of their components. Occasionally, the peptide linkage in a polypeptide is cis, that is, the N–H bond and the carbonyl bond are on the same side of the C–N bond. When a cis linkage is needed, it can be constructed from its component parts—a trigonal nitrogen, a trigonal carbon, and a carbonyl oxygen. The chapter also reviews the space-filling pieces used for these transformations.

Differential Thermal Analysis of Rapid High Pressure Decompositions

Abstract A simple sample handling technique for recording differential thermograms of volatile and/or high pressure producing compounds is described. The calculation of activation energies for several hydrazines and explosives is reported.

CONSTRUCTION OF SIDE CHAIN GROUPS

This chapter highlights the chemical structure of the various amino acid side chains and presents the framework pieces used to construct framework models of side chains. With the exception of proline, construction of these side chains from the listed component parts and their chemical formulas is straightforward. Forming bonds with tygon tubing is preferable to using the more expensive variable fasteners in side-chain construction. This is a practical alternative because the torsion angles in these residues are often not known with great accuracy. Lengths of tygon tubing 1/2 inch (1.27cm) long are appropriate for adequately covering the winged arms while leaving the necessary 4mm between them. The chapter also presents the pieces necessary to transform the framework models of side chains into space-filling forms.

THE PEPTIDE UNIT

This chapter discusses the structure of polypeptide. The basic unit of polypeptide or protein structure is the amino acid. Amino acids are carboxylic acids with an amino group attached to the carbon next to the carboxyl group. This carbon atom is called the 2 α-carbon. Amino acids form polypeptides when the amino group of one amino acid condenses with the carboxyl group of another amino acid to form an amide, or peptide linkage. The polypeptide backbone is comprised of a repeating –C–C–N– unit. That is, peptide linkages alternate with α-carbons. The polypeptides have an amino end or N-terminus and a carboxyl end or C-terminus. In many natural polypeptides, the peptide linkage is planar, that is, the torsion angle of the C–N bond is either 0° or 180°. Most commonly, the oxygen and hydrogen atoms of this linkage aretrans to one another (torsion angle is 180°). This is called the trans-peptide linkage. In the cis-peptide linkage the torsion angle is 0°.

THE TORSION ANGLES ψ AND ϕ

This chapter discusses the polypeptide model construction of torsion angles. As the repeating unit of the polypeptide backbone is a three-atom unit, the torsion angles of the two connecting bonds determine the secondary structure. The peptide linkage is virtually planar in most polypeptides and thus, only two torsion angles, called psi (ψ) and phi (φ), are needed to define the secondary structure of polypeptides. Psi is the torsion angle between the α-carbon and the carbon atom of one of the peptide units. Phi is the torsion angle between the α-carbon and the nitrogen atom of the other peptide unit. A simple mnemonic is helpful in remembering which angle applies to which bond: psi is the angle for the bond between the same atoms C α –C. Phi is the angle for the bond between the two hetero atoms C α –N.

THE ASYMMETRIC α -CARBON ATOM

This chapter discusses the polypeptide model construction of the asymmetric α-carbon atom. The α-carbon atom is asymmetric in all amino acids except glycine. If naturally occurring amino acids were racemates, the side chain could be attached to either of the two remaining arms of the α-carbon atom. However, most naturally occurring amino acids exist in only one stereoisomeric form—the L-configuration. Therefore, only one arm is appropriate for bonding to the side chain. The chapter illustrates the correct bonding arm for L-amino acids. As one proceeds onward from the oxygen atom of one peptide unit to the C–C α bond and toward the nitrogen atom of the C α –N bond of another peptide unit, the α-carbon is located at the top of a bridge. In this configuration, the bonding arm used for L-amino acid side chain is located on the left.

CONSTRUCTION OF AN α -HELIX

This chapter discusses the construction of α-helix. The torsion angle values for the right-handed α-helix are 0 = –57° and ψ = –47°. The construction should be started at the N-terminus with a tetrahedral nitrogen atom, which should be attached with any variable fastener to a tetrahedral carbon atom. This α-carbon is in turn going to bond to the black carbon winged arm of a transpeptide unit to form the C α –C bond. The chapter illustrates the torsion angles in the construction of the N-terminus.

CONSTRUCTON OF β -PLEATED SHEETS

This chapter discusses the construction of α-helix the antiparallel β-pleated sheet and parallel β-pleated sheet. To construct the sheet structure, at least two polypeptide strands should be constructed, each containing at least five peptides. Silicone tubing that is 3.8cm long should be used to form the hydrogen bonds connecting the two strands. To construct a model of the β -parallel pleated sheet, at least two strands must be constructed. In these polypeptides, the φ angles are –119° and the ψ angles are +113°. Silicone tubing should be used for the hydrogen bonds connecting the strands. In this case, the two connected strands run in the same direction.

CONSTRUCTION OF FREE AMINO ACIDS AND POLYPEPTIDE END GROUPS

This chapter discusses the construction of free amino acids and polypeptide end groups. To construct a free amino acid, the tetrahedral α-carbon is connected to a tetrahedral nitrogen piece and a carboxyl piece. It is also attached to a hydrogen atom and a specific side chain, depending on the amino acid being built. One should remember to attach the side chain in the L-configuration. The tetrahedral nitrogen and carboxyl pieces are also used at the two termini of a polypeptide chain. The tetrahedral nitrogen depicts the N-terminus and the carboxyl group, the C-terminus.

COMMON POLYPEPTIDE SECONDARY STRUCTURES

This chapter discusses common polypeptide secondary structures. The polypeptides may be considered as sequences of planar trans-peptide linkages connected through α-carbon atoms. The most stable configuration of these planes occurs when the carbonyl groups of adjacent planes are either aligned or opposed. For each of these possibilities, there are preferred ψ and φ torsion angles. If the carbonyls are aligned on one side of the chain, the N–H bonds are necessarily aligned on the opposite side of the chain. When these bonds are so aligned, the preferred torsional angles allow the polypeptide chain to coil on itself and form a helix. This conformation is stabilized by hydrogen bond formation between carbonyl oxygen atoms and the hydrogens of N–H bonds that are further along the polypeptide backbone. In the β-structure form, the carbonyls of adjacent planes point in opposite directions and the polypeptide chain conformation is an extended, pleated structure. Two or more chains with such conformations can form hydrogen bonds between chains. This can occur in two ways—with the chains going in the same direction or in opposite directions. All of these conformations can easily be constructed from these models by simply dialing the appropriate torsional angles typical of these structures while building the polypeptide backbone.