The document discusses the Ramachandran plot, which shows statistically probable combinations of the phi and psi backbone torsion angles in proteins. It describes how these two angles describe rotations around bonds in the polypeptide backbone and influence protein folding. The plot reveals allowed and disallowed regions based on steric clashes between atoms at different angle combinations. Common structures like alpha helices and beta sheets correspond to allowed regions in the plot.
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
Protein targeting or protein sorting is the mechanism by which a cell transports to the appropriate positions in the cell or outside of it. Both in prokaryotes and eukaryotes, newly synthesized proteins must be delivered to a specific sub-cellular location or exported from the cell for correct activity. This phenomenon is called protein targeting. Protein targeting is necessary for proteins that are destined to work outside the cytoplasm.This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases. In 1970, Günter Blobel conducted experiments on the translocation of proteins across membranes. He was awarded the 1999 Nobel Prize for his findings. He discovered that many proteins have a signal sequence, that is, a short amino acid sequence at one end that functions like a postal code for the target organelle.
Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
Protein targeting or protein sorting is the mechanism by which a cell transports to the appropriate positions in the cell or outside of it. Both in prokaryotes and eukaryotes, newly synthesized proteins must be delivered to a specific sub-cellular location or exported from the cell for correct activity. This phenomenon is called protein targeting. Protein targeting is necessary for proteins that are destined to work outside the cytoplasm.This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases. In 1970, Günter Blobel conducted experiments on the translocation of proteins across membranes. He was awarded the 1999 Nobel Prize for his findings. He discovered that many proteins have a signal sequence, that is, a short amino acid sequence at one end that functions like a postal code for the target organelle.
Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
RAMACHANDRAN PLOT One is to show in principle which values of and angles are ...406SAKSHIPRIYA
This presentation is based on Ramachandran plot, which uses computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations. Plotting the torsional angles in this way graphically shows which combination of angles are possible.
Ramachandran plot for structural validation of protein will give information whether your protein or model protein is allowed or not in three dimensional point of view.
This ppt will help you get through the complete topic for RAMACHANDRAN PLOT in detail .
for detailed explanation , watch the lecture on my youtube channel - BOTANY INSIDER
Gives in detail primary, secondary, tertiary and Quaternary structure of proteins. Gives classification of secondary structure: alpha helix, beta pleated sheet and different types of tight turns and explains most commonly found tight turn in proteins i.e. beta turn. Briefs about the Ramachandran plot of proteins, dihedral or torsion angles and explains why glycine and proline act as alpha helix breakers. Explains tertiary structure of proteins and different covalent and non covalent bonds in the tertiary structure and relative importance of these bonding interactions. Details about the quaternary structure of proteins and explains why hemoglobin is a quaternary protein and insulin is not.
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2. Torsion angles of a protein
• Also known as a dihedral angle
• Formed by three consecutive bonds in a
molecule and
• Defined by the angle created between the
two outer bonds
3. Torsion angles
• The backbone of a protein has three different torsion angles
• Describe the rotations of the polypeptide backbone around the
bonds between
• N-Cα (called Phi, φ)
• Cα-C (called Psi, ψ) and
• The omega-angle (ω) - around the peptide bond between C and N
• ω-bond has a slightly double-bond character and is therefore
almost always 180 degrees
4. Torsion angles
• Torsion angles are
dihedral angles, which
are defined by 4
points in space
• In proteins the two
torsion angles phi and
psi describe the
rotation of the
polypeptide chain
around the two bonds
on both sides of the C
alpha atom
5. Dihedral angle
• The standard IUPAC definition of a dihedral angle is
illustrated in the figure below
• A, B, C and D illustrate the position of the 4 atoms
used to define the dihedral angle
• The rotation takes place around the central B-C bond
• The view on the right is along the B-C bond with
atom A placed at 12 o'clock
• The rotation around the B-C bond is described by the
A-B-D angle shown on the right figure: Positive
angles correspond to clockwise rotation
6. Ramachandran plot
• Phi and psi angles could be varied from -180 to +1800
• Many combinations of these angles are not seen in
proteins
• Some are very common in proteins
• Computer modelling, X-ray crystallographic studies –
reveal the possible combinations of angles
• NMR also used
• Plot of psi vs phi angles – ramachandran plot
7. The Ramachandran Plot
• The Ramachandran plot shows the statistical distribution of
the combinations of the backbone dihedral angles ϕ and ψ
• It also provides an overview of allowed and disallowed
regions of torsion angle values
– serve as an important indicator of the quality of protein
three-dimensional structures
• Torsion angles are among the most important local
structural parameters that control protein folding
8. The Ramachandran Plot
• Ability to predict the Ramachandran angles for a particular
protein, provide ability to predict its 3D folding
• The reason is that these angles provide the flexibility required for
the polypeptide backbone to adopt a certain fold, since ω is
essentially flat and fixed to 180 degrees
– This is due to the partial double-bond character of the peptide
bond which;
– restricts rotation around the C-N bond, placing two successive
alpha-carbons and C, O, N and H between them in one plane
– Thus, rotation of the protein chain can be described as rotation
of the peptide bond planes relative to each other
9. Protein backbone
The psi angle is the angle
around the -CA-C- bond-
can rotate in 3600 (-180-+180)
+ve angle clockwise rotation
The omega angle is the angle
around the -C-N- bond (i.e. the
peptide bond)
The protein backbone can be described in terms of the phi, psi
and omega torsion angles of the bonds:
The phi angle is the angle around the -N-CA- bond - can rotate in 3600
(-180 to +180) +ve angle clockwise rotation
10. The Ramachandran Plot
In a polypeptide the main chain N-Calpha and Calpha-C bonds
relatively are free to rotate. These rotations are represented by
the torsion angles phi and psi, respectively
• G N Ramachandran used computer models of small polypeptides
to systematically vary phi and psi with the objective of finding
stable conformations
• For each conformation, the structure was examined for close
contacts between atoms
• Atoms were treated as hard spheres with dimensions
corresponding to their van der Waals radii
• Therefore, phi and psi angles which cause spheres to collide
correspond to sterically disallowed conformations of the
polypeptide backbone
11. Steric limits of psi and phi angles
• Atoms take up space
• Same space can not be occupied by more than
one atom
• Atoms connected by covalent bonds
• These bonds can not be broken- only rotation
• Only two angles in a residue rotate- psi and phi
• Physical clashes of atoms in 3D space make
many combinations not possible
12. The Ramachandran Plot
In the diagram the white areas
correspond to conformations
where atoms in the
polypeptide come closer than
the sum of their van der Waals
radi
These regions are sterically
disallowed for all amino acids
except glycine which is unique
in that it lacks a side chain
13. The Ramachandran Plot
• The yellow areas show the
allowed regions if slightly
shorter van der Waals radi are
used in the calculation, ie the
atoms are allowed to come a
little closer together
• This brings out an additional
region which corresponds to
the left-handed alpha-helix
The red regions correspond to conformations where there are
no steric clashes, ie these are the allowed regions namely the
alpha-helical and beta-sheet conformations
15. The Ramachandran Plot
• L-amino acids cannot form extended regions of left-
handed helix
– but occasionally individual residues adopt this
conformation
– These residues are usually glycine but can also be
asparagine or aspartate where the side chain forms a
hydrogen bond with the main chain and therefore
stabilises this otherwise unfavourable conformation
– The 3(10) helix occurs close to the upper right of the
alpha-helical region and is on the
edge of allowed region indicating
lower stability
16. 310 helix
• A 310 helix is a type of secondary
structure
• found (often) in proteins and
polypeptides
• Top view of the same helix shown
to the right
• Three carbonyl groups are pointing
upwards towards the viewer
– spaced roughly 120° apart on the
circle
– corresponding to 3.0 amino-acid
residues per turn of the helix
17. The Ramachandran Plot
• Disallowed regions generally involve steric hindrance
between the side chain C-beta methylene group and
main chain atoms
Glycine has no side chain and
therefore can adopt phi and psi
angles in all four quadrants of
the Ramachandran plot
Hence it frequently occurs in
turn regions of proteins where
any other residue would be
sterically hindered
18. Conclusion
• Steric limitations of individual amino acids
decide folding in protein secondary structure
• Folding of proteins is complex and controlled
by psi and phi angles of each amino acid
• Details of the psi and phi angles and the
location in Ramachandran plot help to
predict details about proteins
Editor's Notes
Ramachandran angles -after the Indian physicist who first introduced the Ramachandran plot, (RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN V., J Mol Biol., 7:95-99)
A dihedral angle is the angle between two intersecting planes. In chemistry it is the angle between planes through two sets of three atoms, having two atoms in common. In solid geometry it is defined as the union of a line and two half-planes that have this line as a common edge.
A 310 helix is a type of secondary structure found in proteins and polypeptides. Of the numerous protein secondary structures present, the 310-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 310-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini. Because of the α-helices tendency to consistently fold and unfold, it has been proposed that the 310-helix serves as an intermediary conformation of sorts, and provides insight into the initiation of α-helix folding.
A 310 helix is a type of secondary structure found in proteins and polypeptides. Of the numerous protein secondary structures present, the 310-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 310-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini. Because of the α-helices tendency to consistently fold and unfold, it has been proposed that the 310-helix serves as an intermediary conformation of sorts, and provides insight into the initiation of α-helix folding.
