The document discusses the Ramachandran plot, which is a plot of the phi (φ) angle versus the psi (ψ) angle of amino acid residues in protein structures. It explains that these two angles are limited by steric constraints from the atoms in the protein backbone. The allowed and disallowed regions in the Ramachandran plot correspond to conformations where backbone atoms are too close or clashing versus conformations where they have sufficient space. Most protein structures fall within the allowed regions, helping explain their stable secondary structures.
Describes various aspects of Ramachandran plot. Different torsion angles are described with clear figures. How protein folding is affected by torsion angles is also explained.
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.
Describes various aspects of Ramachandran plot. Different torsion angles are described with clear figures. How protein folding is affected by torsion angles is also explained.
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.
Zymography is an electrophoretic technique for the detection of hydrolytic enzymes, based on the substrate repertoire of the enzyme. ... Zymography also refers to a collection of related, fermented products, considered as a body of work.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
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.
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
Zymography is an electrophoretic technique for the detection of hydrolytic enzymes, based on the substrate repertoire of the enzyme. ... Zymography also refers to a collection of related, fermented products, considered as a body of work.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
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.
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
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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.
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What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
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Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
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Ramachandran plot
1. Ramachandran Plot
By
Mrs Sanchita Choubey
(M.Sc., PGDCR, Pursuing Ph. D)
Assistant Professor of Microbiology
Dr. D Y Patil Arts Commerce and Science College Pimpri, Pune
2. CONTENTS
2
Introduction
Limits on Rotation inAmides
The ψ (psi)Angle
The φ (phi)Angle
The Ramachandran Plot
Steric Limits of ψ and φ
Conclusion
References
3. INTRODUCTION
The secondary structures that polypeptides can adopt in
proteins are governed by hydrogen bonding
interactions between the electronegative carbonyl
oxygen atoms and the electropositive amide hydrogen
atoms in the backbone chain of the molecule.
These hydrogen-bonding interactions can form the
framework that stabilizes the secondary structure.
Many secondary structures with reasonable hydrogen
bonding networks could be proposed but we see only a
few possibilities in polypeptides composed of L-amino
acids (proteins).
Most of the possible secondary structures are not
possible due to limits on the configuration of the
backbone of each amino acid residue.
Understanding these limitations will help you to
understandthe secondary structures of proteins. 3
5. Limits on Rotation in Amides
We do not have as many degrees of freedom as we have
bonds.
The amide bonds are held in a planar orientation due to
orbital overlap between the π-orbitals of the SP2
hybridized atoms of the carbonyl group and the π-orbital of
the SP2 hybridized amine group.
This distributed π-orbital system resists rotation, as the
orbital overlap would have to be broken.
The distributed nature of the system also makes the amide
bond resistant to hydrolysis.
The amide group will prefer to have all atoms connected to it
in the same plane as the amide bond (no rotation).
This can result in a ‘cis’ or ‘trans’ configuration.
Due to steric and electronic reasons the ‘trans’
configuration is the predominant form for the amide bond.
Note the steric clash between the side chain groups in5the
‘cis’ form.
6. So we can look at a polypeptide chain as a
series of planar structures connected by
swivel joints at the α-carbons of each
amino acid residue.
The two atoms of each amide bond and the
four atoms connected to them are coplanar
for each individual amide bond.
Any two planar amide groups share a
common atom – the α-carbon of an amino
acid residue.
These swivel joints have two connections
that can rotate freely.
6
7. The ψ (psi) Angle
The bond from the α-carbon to the carbonyl group (at
the C-terminus) of the amino acid residue can rotate and
turn the whole plane of the amide group, which includes
the carbonyl carbon, in a 360-degree range.
This angle is measured by looking along that bond with
the carbon of the carbonyl group in the rear and the α-
carbon to the front.
We measure the apparent angle between the two bonds to
nitrogen that you can see coming out of the axis of the
CαC(C=O) bond.
This angle is labeled ψ (psi) and is measured from –180°
to +180° with the positive direction being when you turn
the rear group clockwise so that the rear nitrogen bond is
clockwise of the front nitrogen bond (or when you turn the
front group counterclockwise so that the rear nitrogen
bond Is clockwise of the front.) 7
9. The φ (phi) Angle
9
The bond from the nitrogen (at the N-terminus) to the α-
carbon of the amino acid residue can rotate and turn the
whole plane of the other amide group, which includes the
nitrogen, in a 360-degree range.
This angle is measured by looking along that bond with the
nitrogen atom in front and the α-carbon to the rear.
We measure the apparent angle between the two bonds to
the carbonyl carbons that you can see coming out of the axis
of the NCα bond.
This angle is labeled φ (phi) and is measured from –180° to
+180° with the positive direction being when you turn the
rear group clockwise so that the rear carbonyl bond is
clockwise of the front carbonyl bond (or when you turn the
front group counterclockwise so that the rear carbonyl bond
is clockwise of the front.)
11. The Ramachandran Plot
11
We can vary ψ from –180° to 180° and we can vary φ from –
180° to 180° (that is 360° of rotation for each).
But many combinations of these angles are almost never
seen and others are very, very common in proteins.
We will obtain a data set for the positions of each atom in
space. We can get such data from one of the several
depositories of protein structural data.
We will use X-ray crystallography data, as it is the most
precise. (Although it may not be completely accurate, as
crystal packing forces usually distort proteins slightly.
12. The Ramachandran Plot
12
NMR data for proteins in solution are not very precise but
are considered to be more accurate as the protein is in its
native environment.
We can take this data and detect the amino acid residues
(this is usually done for us as the X-ray crystallography
“.PDB” data format labels all atoms and assigns them to
residues).
A computer program can take a “.PDB” file and report the of
ψ and φ angles for each and every residue.
A plot of ψ vs. φ is called a Ramachandran plot.
14. Steric Limits of ψ and φ
Atoms take up space and cannot occupy the same
space at the same time.
Covalent bonds connect them and these bonds cannot
be broken.
So the movements that we are concerned withinvolve
rotations only.
There are only two angles that rotate in a given
residue, ψ and φ.
But not all combinations are possible due to
physical clashes of atoms in 3-dimensional space.
These physical clashes are called steric
interactions
and the limit the available values for ψ and φ.
14
16. 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
17. CONCLUSION
17
Understanding the steric limitations in individual amino
acid residues reveals how these limitations result in the
observed types of secondary structures found in
nature.
The complex folding of proteins is controlled, in a large
part, by the limitations on the ψ and φ angles available
to each amino acid residue.
If one inspects the ψ and φ angle combinations that exist
in idealized secondary structures we can place the sites
in a Ramachandran plot where we would expect to see
data related to these structures.
In a real protein we would expect data points from these
defined secondary structures to appear near the ideal
location.
18. Dihedral angles, translation distances and number
of residues per turn for regular secondarystructure
17
conformations