Peptide helical macro-dipole moment

Figure 2.10: Comparative schematic representation of α-helix with a macro-dipole moment from N-to-C terminus (A); a 14-helix with an overall macro-dipole moment from C-to-N terminus, i.e., opposite to that of α-helix (B); an alternate 10/12-helix with overall nullified zero macro-dipole moment (C)

Secondary Structure Rise (Å) Pitch (Å) Residues/turn

α-helix^[118] 1.5 5.4 3.6

14-helix^[99] 1.7 5.2 3.1

12-helix^[119] 2.2 5.9 2.7

10/12-helix^[92] 2.1 5.7 2.7

Table: 1: At-a-glance geometrical parameters for different types of β-peptides

2.2.3 Peptide helical macro-dipole moment

Throughout the scientific literature on protein research of the last thirty years, the α-helix dipole is mentioned in a number of cases where its partial charge on both the C-terminal and the N-terminal ends is thought to be involved in various biological processes on a molecular level. In order to understand the cause of this dipole moment, one must look at the structure and the geometry of the α-helix. The α-helix is a right-handed coiled structure. Each amino acid makes a turn of about 100 degrees and hence it requires 3.6 residues to make a full turn. Amino acids that wind around the axis form hydrogen bounds with each other. The N-H group of each amino acid forms a hydrogen bond with the C=O of the amino acid that is located four places earlier in the helix. The vast number of hydrogen bonds that is formed is actually the underlying reason for the forming of this secondary protein structure. Although the principles behind the occurrence of the helix dipole have been described earlier, Hol first reviewed its role in protein structure and function in 1985^[114]. He states that the helix dipole originates in the dipole of the individual peptide unit. The charge distribution within such a unit is depicted in Figure 2.11. Its direction

A B C

is parallel to the N-H and C=O bonds. It has been shown that in a α-helix around 97% of all peptide dipole moments point in the direction of the helix axis, the dipole is therefore quite insensitive to the φ and ψ angles. The C=O groups are in a slightly upward direction (toward the C-terminus) and the N-H groups are in a downward direction (toward the N-terminus) and this gives rise to a small dipole. The aggregate effect of all individual dipoles in a α-helix gives rise to a net negative dipole moment at the C-terminal end, and a positive dipole moment at the N-terminal end of the helix. The dipole moment of an individual peptide unit is about 3.46 Debye (D) which equals 0.72 e Å or 0.5 e per 1.5 Å. Since the axial shift per residue in a α-helix is also 1.5 Å, all dipoles cancel out except for the C- and N-terminal ones.

Figure 2.11: Excess charge distribution in a peptide unit showing the resultant dipole moment (μ)

[114]

Hence, the origin of helical dipole moment in α-peptides has long been explored. However, unlike the α-peptides, the same for the β-peptides still lack in experimental investigations.

Synthetic β-peptides represent a particularly intriguing class of molecules for fundamental studies in the area of peptidomimetics. Being the oligomers of β-amino acids, β-peptides offer considerable control over the stability of the secondary structure. The β -peptides are observed to fold into various helical secondary structures among which the 14-helical and 12-helical structures are more commonly found. The nomenclature of these helices is based on the number of atoms in the characteristic hydrogen bonds. For example, a β-peptide 14-helix is defined by i, i-2 C=O···H-N hydrogen bonds that contain 14 atoms and 12 helix by i, i+3 C=O···H-N hydrogen bonds containing 12 atoms. In both these helices, just like the α-peptides, all the individual dipoles cancel out and remains of the ones at the C- and N-terminals. The amide bonds are uniformly aligned parallel to the helical axis and this gives rise to an overall net macrodipole

μ

moment in 14- and 12-helices. Nevertheless, unlike the α-peptides, the net helical macrodipole moments for these two β-peptide helices are from C- to N-terminal. Therefore, these two commonly found β-peptide helices exhibit an inverted overall helical macrodipole moment. On the other hand, a third type of helical secondary structure is also found that is composed of alternating 10- and 12-membered hydrogen bonded rings yielding an alternate 10/12-helical secondary structure. The 10-membered ring is defined by i, i-1 C=O· · ·H-N and the 12-membered ring by i, i+3 C=O· · ·H-N. In 12-membered hydrogen bonded ring, the amides are aligned parallel to the helical axis (just as the 12-helical secondary structure). However, in case of the 10-membered ring, unlike all the other types of helices, the amides are aligned almost perpendicular to the helical axis. Therefore, the alternate parallel and perpendicular orientation of the amides in 10/12-helix ultimately nullifies the helical dipole moments and gives rise to a unique peptide secondary structure with zero macrodipole moment. This unique feature of the alternate 10/12-helical secondary structure of the β -peptides with no macrodipole moment draws scientific interest in the field of verification of any effect of helical macrodipole moment in different physico-chemical properties the peptides. The experimental knowledge in this field would shed light and contribute significantly in various aspects of peptidomimetics. As for example, it has long been reviewed by Hol et. al. that one in four enzymes of known conformation has an α-helical macrodipole moment that affects the electric field in its active sites. ^[114] Hol et. al. also investigated elaborately the anion-binding preferences of α-helices depending on their helical macrodipole moments. However, unlike the α-peptides, accurate experimental estimation of helical marodipole moments for any of the secondary helical structures of the β-peptides is still yet to be done. Although there have a several postulates and theoretical studies based on molecular dynamic simulations published indicating the possible role of the helical macrodipole moment of the β -peptides in regulation of various physico-chemical and biochemical properties including, dipole induced self-assembly^[113], intra-helical aggregation^[115], insertion into lipid-membranes^[112], voltage-gating in relation of ion-channel formation,[116, 117] but there is hardly any experimental report on the effect of helical macrodipole moment in regulating these properties. The prime reason behind this unavailability of experimental investigations is the synthesis of the zero-dipole β -peptides with alternating 10/12-helical secondary structure. It is necessary to experimentally access the 10/12-helical β -peptides with zero macrodipole moment and compare the results of physico-chemical or biochemical experiments with that of the other types of β -peptides, such as, 14-helical, that have a net macrodipole moment. Only after the efficient comparison, it is possible to shed light on any possible effect of helical macrodipole moment on the mentioned physico-chemical or biochemical properties experimentally. So, it is the main objective of this project to successfully design and synthesize synthetic β-peptides with

nullified helical macrodipole moment and shed light on the effect of the latter on the lipid-membrane insertion. Since, the project mainly deals with the development of β-peptide based artificial transmembrane domain systems, the fundamental knowledge on the effect of helical macrodipole moment on the membrane insertion is of the greater interests.