1. Protein structure
and modeling
Preston
University
Islam abad
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2. Introduction
• Protein
• Function of proteins
• Enzymes
• Structures
• Catalysts
• Transportation
• Regulation
• Signaling
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3. Amino acids
• Amino acids basic units of proteins
• Chiral carbon
• Side chain
• Hydrogen group
• Amino group
• Carboxylic group
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4. Protein sequences: amino acids
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8. Codes for amino acids
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9. Protein
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure
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10. Secondary structures
• Structures formed via introduction of hydrogen bonding in the
linear polypeptide chain
• Alpha helices
• Beta sheets
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11. Alpha helices
• Right hand-coiled or spiral conformation (helix) in which every
backbone N-H group donates a hydrogen bond to the backbone
C=O group of the amino acid four residues earlier ( hydrogen
bonding).
• Among types of local structure in proteins, the α-helix is the most
regular and the most predictable from sequence, as well as the
most prevalent.
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13. Beta sheets
• The β sheet (also β-pleated sheet) is the second form of
regular secondary structure in proteins. It is less common
than the alpha helix.
• Beta sheets consist of beta strands connected laterally by at
least two or three backbone hydrogen bonds, forming a
generally twisted, pleated sheet.
• A beta strand (also β strand) is a stretch of polypeptide
chain typically 3 to 10 amino acids long with backbone in an
almost fully extended conformation.
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14. Parallel beta sheet
Anti parallel beta sheet
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15. Tertiary structure
• The term protein tertiary structure refers to a protein's
geometric shape. The tertiary structure will have a single
polypeptide chain "backbone" with one or more protein
secondary structures, the protein domains.
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17. Conformational parameters for
secondary structure of a protein
• Dihedral angles: in proteins the A.A joint is specific in its
orientation which determines the conformation of the
protein.
• The conformation of the protein could then be elucidated via
the angles in the parent chain and not the side chain of the
protein
• The angle Phi φ is present at the C alpha to Nitrogen of amino
group in the polypeptide
• The angle Psi ψ is present at the C alpha to carbon of
carboxylic group in the polypeptide
• The angles phi and psi should be considered as 180 degrees
when the polypeptide is in fully extended conformation
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18. Ramachandran plot
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• There are certain permitted values
for these angles.
• As if the values are not appropriate
there might be steric hindrance and
the conformation might get
distorted.
• The protein might also get non
functional

19. • A Ramachandran plot can be used in two different ways.
• One is to show in theory which values, or conformations, of
the ψ and φ angles are possible for an amino-acid residue in a
protein .
• A second is to show the empirical distribution of data points
observed in a single structure in usage for structure validation,
or else in a database of many structures
• Either case is usually shown against outlines for the
theoretically favored regions.
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20. Ramachandran Plot
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21. Hydropathy plot
• A hydropathy plot is a quantitative analysis of the degree of
hydrophobicity or hydrophilicity of amino acids of a protein.
• It is used to characterize or identify possible structure or
domains of a protein.
• If more hydrophobic residues are present in a plot this means
that the protein is a trans membrane protein and domain
refers to the inner side of the membrane that spans the
membrane multiple times.
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22. • The plot has amino acid sequence of a protein on its x-axis
• Degree of hydrophobicity and hydrophilicity on its y-axis
• There is a number of methods to measure the degree of
interaction of polar solvents such as water with specific amino
acids.
• For instance, the Kyte-Doolittle scale indicates hydrophobic
amino acids, whereas the Hopp-Woods scale measures
hydrophilic residues.
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23. • Analyzing the shape of the plot gives information about partial
structure of the protein.
• For instance, if a stretch of about 20 amino acids shows
positive for hydrophobicity, these amino acids may be part of
alpha-helix spanning across a lipid bilayer, which is composed
of hydrophobic fatty acids.
• On the converse, amino acids with high hydrophilicity indicate
that these residues are in contact with solvent, or water, and
that they are therefore likely to reside on the outer surface of
the protein.
• Expasy protscale - could be used to construct a hydropathy
plot instantaneously 23

24. Expasy – protscale
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aquaporin

29. Methods of protein structure
and modeling
Threading
or fold
recognition
Ab initio/
De novo
method
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30. 1)Threading
• There might be a structural similarity in two proteins with
almost less than ten percent of the sequence similarity
• When sequence based comparison methods are not much
efficient to recognize the folds and domains in the target
sequence then we proceed with the threading
• Threading is the method by which a library of unique
structures is searched for structure analogues to the target
sequence, and is based on the theory that there may be only a
distinct number of folds
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31. Basic components of folding
Representation of
the query
sequence
Representation of
the protein
structural models
Objective function
Aligning a
sequence to a
model
Selecting a model
from a library
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32. Representation of the query
sequence
• Similar protein sequence leads to the similar protein structure
• Sequences similar to the query sequence are carrying
information about the 3D structure of the query sequence
• The algorithms are also there to develop the different
representation
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33. Representation of the protein
structural models
• Protein structure is determined by all the non hydrogen atoms
in their 3D conformation
• The 3D coordinates in the soft wares used for threading
purpose are more well suited to the abstract protein structure
and give almost a view which is just like the original 3D protein
structures
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34. Objective function
• The 3D data deposited in the databases like PDB is analyzed
via the different statistical protocols
• These analyzed data are now referred to as knowledge based
potentials or empirical potentials
• In the case of non-linear models the other name is contact
potentials etc
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35. Aligning a sequence to a model
• The goal of threading alignment algorithm is to find an
optimal match for the query sequence to the best suited
sample protein sequence
• The sequence structure algorithms can be done to find the
best suited match
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36. Selecting a model from a
library
• The different models which result as a base of alignments of
the sequences and structures would lead to multiple results
• The best result with the highest score would be selected to
model the protein structure
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37. 2) Ab initio method
• Ab initio structure prediction leads to the protein structure
determination by the protein sequence alone
• The free energy estimation of all the molecules present in the
amino acid sequence of the protein is also done
independently
• The two key components of the de novo methods are the
procedure for the efficiently carrying the conformational
search and the free energy estimation function used for
evaluating the possible conformations.
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38. Ab-initio method
Advantages
• Ab-initio approach can
be applied to model any
sequence
Disadvantages
• Low resolution models
• Limited number of
residues of less than 100
amino acids could be
modeled only
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39. Thanks 
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40. Signal peptide prediction
• A signal peptide which is also sometimes referred to as signal
sequence, leader sequence or leader peptide is a short 5-30
amino acids long peptide present at the N-terminus of the
majority of newly synthesized proteins.
• These proteins are destined towards the secretory pathway.
• These proteins include those that reside either inside certain
organelles (the endoplasmic reticulum, Golgi or endosomes),
secreted from the cell, or inserted into most cellular
membranes.
• Signal peptide version 4 has been used to detect the presence
of the signal peptides
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