Protein Structure Basics

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Chapter 12 Protein Structure Basics
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• 20 naturally occurring amino acids
• Free amino group (-NH2)
• Free carboxyl group (-COOH)
• Both groups linked to a central carbon (?C)

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Dihedral Angles
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Ramachandran plot
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Hierarchy

• Primary structure
• Linear sequence of amino acids
• Secondary structure
• Local conformation of the peptide chain
• Stabilized by H-bonds between NH and CO of
  different residues
• Tertiary structure
• 3 dimensional arrangement of all secondary
  structure elements and connecting regions
• Quaternary structure
• Assembly of several polypeptide chains into a
  protein complex

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Stabilizing forces
Secondary to Quaternary structure maintained by
non-covalent forces Electrostatic
interactions Excess negative charge balanced by
positive charge in another region Salt bridge Van
der Waals forces Induced dipole Hydrogen
bonding Sharing of proton by two electron
negative atoms Short distance (lt3Å)
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? Helices

• 3.6 aa per turn
• ?60º
• ?45º
• A, Q, L M frequent
• P, G, Y scarce

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?-Sheet

• H-bonded ?-strands
• Parallel
• Anti-parallel

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Coiled-coil
1KD8
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Tertiary Structures
Globular proteins Compact Polar and hydrophilic
aa on the outside Hydrophobic amino acids on the
inside Integral Membrane Proteins Exist in
lipid bilayers ? Helix segments Connecting
loopsliein aqueous phase
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X-ray crystallography

• Protein crystallized
• Illuminated with X-ray beam, and diffraction
  pattern recorded
• Diffraction pattern converted to electron density
  map by Fourier transformation
• To interpret 3D structure from 2D electron
  density ,map require phase information
• Molecular replacement
• Use homologous protein structure as template
• Multiple isomorphous replacement
• Compare e- density changes in protein crystals
  containing strongly diffracting heavy metals
• Model with amino acid residues that best fit the
  density map

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NMR

• Proteins labeled with 13C or 15N
• Radiofrequency radiation used to induce nuclear
  spin state transitions in a magnetic field
• Interactions between spinning isotope pairs
  produce radio signal peaks that correlate with
  distance between them
• Information on distanmces between all pairs allow
  protein model to be derived
• NMR determines structure in solution
• Dynamic conformations means that 20-40 structures
  satisfy distance constrains
• Can only solve lt200aa proteins

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Protein Structure Database
x,y,z position of each atom in crystal http//www.
rcsb.org/pdb/
Total folds
Total proteins
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PDB File Format
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Other structure file formats

• mmCIF
• Macromolecular crystallographic information file
• Similar to relational database
• Each field assigned a tag and linked to another
  field
• MMDB
• Molecular modeling database
• ASN.1 format
• Nested hierarchy

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Chapter 13 Protein structure visualization,
comparison and classification
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Download and install Jmol http//jmol.sourceforge
.net/
wireframe
Ball-and-stick
Cartoon
CPK (Corey, Pauling and Koltan)
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Rendered in POV-Ray http//www.povray.org/
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Protein structure comparisons
Comparing two protein structures is a fundamental
technique in protein analysis Finding remote
homologs Proteins structures can be very similar
even if sequence identity is very low (lt20)
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Intermolecular method
Identify equivalent residues Translate one
structure relative to the other unlik both occupy
same space Rotate one structure relative to
other, and continuously calcuilate distances
between equivalent residues Root mean square
deviation Larger proteins have larger
RMSD Difficult to identify equivalent
residues Discard regions outside secondary
structures Work with 6-9 residue
fragments Dynamic programming, starting with few
equivalent residues
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Intramolecular method

• Calculate a distance matrix of all residue
  distances in two proteins, separately
• Translate two matrices until differences are
  minimal
• Good to identify similar secondary structure
  regions in two proteins

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Multiple structure alignment
Compare structures in pairwise fashion,
generating matrices based on RSMD
scores Construct phylogenetic tree Two must
similar structures are realigned Median structure
created to which other more distant structures
are systematically aligned DALI Distances
calculated from intra-molecular ?C distances
matrices Matrices are aligned to find local
structural similarities Calculate Z-score CE
Combinatorial Extension Like DALI, but uses every
8th residue VAST Vector Alignment Search
Tool Uses intra- and intermolecular
approaches SSAP Intramolecular based
methods Dynamic programming to find residue path
with optimal score STAMP Intermolecular
approach, using dynamic programming
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Protein structure classification

• Classification systems allows identification of
  relationships between structures
• Provide evolutionary view of all structures
• Newly solved structures can be fitted into
  hierarchy, defining possible functions
• SCOP (Structural Classification of Proteins)
• Manual examination of structures
• Classes, folds, families and super families
• Families share high sequence homology
• Super families may have common ancestral proteins
• Folds look at order and connectivity of secondary
  structures, may not be evolutionary related
• Classes folds with similar core structures
  all-?. all-?, ? and ?, etc.
• CATH (Class, architecture, topology and homologs)
• Uses automatic assignment with SSAP as well as
  manual comparison
• Class similar to SCOP
• Architecture intermediate between SCOP fold and
  class overall packaging and arrangement of
  secondary structures without regard for
  connectivity
• Topology SCOP fold
• Homologous superfamily and homologous family
  equivalent to SCOP super family and family