Protein structure

Amino acids

Amino acids: R group properties

Amino acids: R group properties

Hydro-pathy/phobicity/philicityHydro-pathy/phobicity/philicity

• One of the most commonly used properties is the suitability of an amino acid for an aqueous environment

• Hydropathy & Hydrophobicity– degree to which something is “water

hating” or “water fearing”

• Hydrophilicity– degree to which something is “water loving”

Hydro-pathy/phobicity/philicity Analysis

Hydro-pathy/phobicity/philicity Analysis

• Goal: Obtain quantitative descriptions of the degree to which regions of a protein are likely to be exposed to aqueous solvents

• Starting point: Tables of propensities of each amino acid

Hydro-pathy/phobicity/philicity Analysis

Hydro-pathy/phobicity/philicity Analysis

• Goal: Obtain quantitative descriptions of the degree to which regions of a protein are likely to be exposed to aqueous solvents

• Starting point: Tables of propensities of each amino acid

Kyte-Doolittle hydropathyKyte-Doolittle hydropathyAminoAcid

Index AminoAcid

Index

R -4.5 S -0.8K -3.9 T -0.7D -3.5 G -0.4Q -3.5 A 1.8N -3.5 M 1.9E -3.5 C 2.5H -3.2 F 2.8P -1.6 L 3.8Y -1.3 V 4.2W -0.9 I 4.5

Basic Hydropathy/Hydrophilicity Plot

Basic Hydropathy/Hydrophilicity Plot• Calculate average hydropathy over a

window (e.g., 7 amino acids) and slide window until entire sequence has been analyzed

• Plot average for each window versus position of window in sequence

Example Hydrophilicity PlotExample Hydrophilicity Plot

This plot is for a tubulin, a soluble cytoplasmic protein. Regions with high hydrophilicity are likely to be exposed to the solvent (cytoplasm), while those with low hydrophilicity are likely to be internal or interacting with other proteins.

Peptide bonds

Peptide bonds

Peptide bonds

Torsion angles

Alpha helix

Rule of thumbs

Hydrogen bonding

• 3.1.1 alpha helix• The alpha helix is the most abundant helical conformation found in globular proteins accounting

for 32-38% of all residues (Kabsch & Sander, 1983; Creighton, 1993). The average length of an alpha helix is 10 residues as taken from surveys of this structural database. The average dihedral angles phi and psi (-64 +/- 7, -41 +/- 7) also obtained from these surveys are found to differ slightly from the geometrically pure alpha helix (-57.8, -47.0). The abundance of this particular form of secondary structure stems from the following properties:

• the phi and psi angles of the alpha helix (lie in the center of an allowed, minimum energy region of the Ramachandran (phi, psi) map.

• the dipoles of hydrogen bonding backbone atoms are in near perfect alignment. • the radius of the helix allows for favorable van der Waals interactions across the helical axis. • side chains are well staggered minimizing steric interference. • A good look at a geometrically pure alpha helix is afforded by the CPK representation shown in

Figure 2 . Notice how all amide protons point toward the N-terminus (down) and all carbonyl oxygens point toward the C-terminus (up). The repeating nature of the phi, psi pairs ensure this orientation. Hydrogen bonds within an alpha-helix also display repeating pattern in which the backbone C=O of residue i hydrogen bonds to the backbone HN of residue i+4. Looking at the helix along the helical axis from the C-terminus (top), you can see the four carbonyl oxygens of the last turn of the helix and the dispersion of sidechains. Residues in positions (i, i+3) and (i, i+4) are positioned in such a way as to force interaction of their sidechains. This can have a stabilizing effect if the residues are of opposite charge or are both hydrophobic (see "stereochemical" ). Interaction between aromatic rings (Phe) at position (i) and His at position (i+4) appears to have a stabilizing effect on the helical conformation of the C-peptide of ribonuclease in solution (Armstrong et al., 1993).

Beta-sheet

Types of beta sheets

Antiparallel

Twists with beta-sheets

The Ramachandran Plot

Reverse turns

Ramachandran plot: turn

The beta-hairpin turn

Two residue beta-hairpin turns

Glossary• primary structure: The linear amino acid sequence of the

polypeptide chain including post-translational modifications and disulfide bonds.

• secondary structure: Local structure of linear segments of the polypeptide backbone atoms without regard to the conformation of the side chains.

• super secondary structure (motif): Associations of secondary structural elements through sidechain interactions.

• domains: Associations of lower order structure • tertiary structure: The three-dimensional arrangement of all atoms

in a single polypeptide chain. • quaternary structure: The arrangement of separate polypeptide

chains (subunits) into the functional protein.

Amphipathic helix

amphipathic helix: with a hydrophobic face (to satisfy the core) and a hydrophilic face (to interact favorably with the solvent).

Helical Wheel for Prion Protein

Helical Wheel for Prion Protein

Levels of organizations

Domains

"Within a single subunit [polypeptide chain], contiguous portions of the polypeptide chain frequently fold into compact, local semiindependent units called domains." - Richardson, 1981

SCOP database

• Classification of proteins– Alpha– Beta– Alpha / beta– Alpha + beta– Multidomain– Membrane / cell surface

CATH• Class, C-level

Class is determined according to the secondary structure composition and packing within the structure. It can be assigned automatically for over 90% of the known structures using the method of Michie et al. (1996). For the remainder, manual inspection is used and where necessary information from the literature taken into account. Three major classes are recognised; mainly-alpha, mainly-beta and alpha-beta. This last class (alpha-beta) includes both alternating alpha/beta structures and alpha+beta structures, as originally defined by Levitt and Chothia (1976). A fourth class is also identified which contains protein domains which have low secondary structure content.

• Architecture, A-level This describes the overall shape of the domain structure as determined by the orientations of the secondary structures but ignores the connectivity between the secondary structures. It is currently assigned manually using a simple description of the secondary structure arrangement e.g. barrel or 3-layer sandwich. Reference is made to the literature for well-known architectures (e.g the beta-propellor or alpha four helix bundle). Procedures are being developed for automating this step.

• Topology (Fold family), T-level Structures are grouped into fold families at this level depending on both the overall shape and connectivity of the secondary structures. This is done using the structure comparison algorithm SSAP (Taylor & Orengo (1989)). Parameters for clustering domains into the same fold family have been determined by empirical trials throughout the databank (Orengo et al. (1992), Orengo et al. (1993)). Structures which have a SSAP score of 70 and where at least 60% of the larger protein matches the smaller protein are assigned to the same T level or fold family.

• Some fold families are very highly populated (Orengo et al. (1994)) particularly within the mainly-beta 2-layer sandwich architectures and the alpha-beta 3-layer sandwich architectures. In order to appreciate the structural relationships within these families more easily, they are currently subdivided using a higher cutoff on the SSAP score (75 for some mainly-beta and alpha-beta families, 80 for some mainly-alpha families, together with a higher overlap requirement (70%)).

• Homologous Superfamily, H-level This level groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous. Similarities are identified first by sequence comparisons and subsequently by structure comparison using SSAP. Structures are clustered into the same homologous superfamily if they satisfy one of the following criteria:

• Sequence identity >= 35%, 60% of larger structure equivalent to smaller • SSAP score >= 80.0 and sequence identity >= 20%

60% of larger structure equivalent to smaller • SSAP score >= 80.0, 60% of larger structure equivalent to smaller, and

domains which have related functions • Sequence families, S-level

• Structures within each H-level are further clustered on sequence identity. Domains clustered in the same sequence families have sequence identities >35% (with at least 60% of the larger domain equivalent to the smaller), indicating highly similar structures and functions.

CATH

FSSP

• Fold classification based on Structure-Structure alignment of Proteins (FSSP)

• Uses DALI (Distance Alignment tool)