Itis formed between two amino acids when an amide bond is situated on both sidesby carbon atoms. Peptide bonds show how the electrons are distributed betweenatoms because of their differences in hybridizations in their bonding orbitalsand the polarity of atoms. If the peptide group consists any of these fouratoms, two are more electronegative (O and N) and two of them should be lesselectronegative atoms (C and H) then we can say the structure is in resonance.
Thus,it forms double bond partially with an intermediate bond length. Polypeptidechains which are across the bond can be in two forms cis and trans. Additionalconsequences are added to the polypeptide structure when peptide bond hasplanarity. Bond Rotation and it’sRestrictionsThereare some restricted and free rotations in peptide bonds.
These two rotationsplay a pivotal role for the polypeptide structure. On the Ramachandran plot wecan see G space for each amino acid. Restrictions are reserved for somebranched residues and for the G space only little fraction is allowed.
Betweenthe helix and strand region there is an energy barrier. Most of the residuesare allowed in both these regions but also the conversion is restricted betweenhelical and strand region. In large cases planarity is slightly deviated intofractions from the peptide bond. Angles of peptide bond effect enlarging thespace for G space and it reduces the strand barrier. In protein structures,some residues are tending to have polar residues which are small, and they areoutside the allowed regions.
SecondaryStructuresSterichinderance between the backbone and side chain is due to the restrictions on Gspace. And that’s how helical and strand regions are originated in secondarystructures. No sequence dependence is allowed on the two regions because grestrictions are more happened in between the residues not within each separately.These secondary structures are favorable for the chain under all conditions andthey are independent about bonding.
Helix is having spring structure and it isright handed. Opposite charges get neutralize in the middle of helix when pitchand dimensions of the helix bring dipole moments of peptide residues intoproximity. But the peptide dipole cannot be neutralized at the ends and theyresult in net helix macrodipole. Maybe these charges get neutralized by sidechains which are nearer.
When amide proton is brought into the proximity bypitch and dimensional helix hydrogen bond is formed with carbonyl oxygen ofresidue. Helical segments are in the central part not at the end when peptidegroup hydrogen bonds are satisfied. But the structure is saying that all thehydrogen bond acceptors and donors are highly populated in helical segments ofproteins. G restriction plays a role in helical confirmation by enhancing theconcentrations of acceptors and donors.Strands are alsoimportant in these secondary protein structures.
In this structures dipolemoment is altered because these structures are extended. G space is larger thanthe G steric hinderance because it is reduced in the strand region. Unlikehelical structures the hydrogen bond donors and acceptors are not satisfied butthey have an independent existence.
These strand segments can also come fromthe distant segments of the chain. And these sheets can occur only in onestrand and they have parallel and antiparallel mixture of the two strands. Thus,when forming hairpin structure chain structures and residues which are distinctbrought at the ends of N and C terminals.
So, this may be the reason strandsheet can be called as tertiary structure