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Motifs of Protein Structure

Protein molecules are organized in a structural hierarchy

Formation of secondary structures ! Alpha helices Beta Sheets Characterized by- main chain NH and CO groups participating in H-bonds to each other. Formed when a number of consecutive residues have the same phi and psi angles.

Alpha Helices
The C=O (or N-H) of n residue is hydrogen bonded to NH (or C=O) of n+4 residue Every 3.6 residues make one turn The distance between two turns is 5.4 Alpha helices are formed when a stretch of consecutive residues all having the phi,psi angle pair approax -60 & -50 , corresponding to the allowed region of Ramchandran plot.

a-helices
H bond between residues i, i+4

Rise per residue, d = 1.5

# of residues per turn, n = 3.6

Pitch of helix, n.d = 5.4

The alpha-helix has a dipole moment

The dipole of a peptide unit. Numbers in boxes give the approximate fractional charges of the atoms of the peptide unit

The Dipoles of peptide units are aligned along the helical axis

Some amino acids are preferred in alpha-helices


Good helix formers: ALA , GLU, LEU , MET

Less Preferred: PRO , GLY, TYR, SER

Helical Wheel: Each residue can be plotted every 360/3.6=100 around a circle or spiral

Helical Wheel Plot

Alpha helix can be Right-handed or Left Handed. BUT, left handed helix not possible for L-aminoacids due to close approach of the side chains and CO group.

Right handed most commonly observed in proteins.

a-helix from one continuous region; b-sheet from several regions of the chain. b-strands, 5-10 residues long

b-sheet

Antiparallel: HBs perpendicular to strands, narrowly spaced bond pairs alternated with widely spaced pairs

pleated side chains point up and down alternatively

Parallel sheet

Mixed sheet

Loop regions are at the surface of protein molecules

Secondary structure elements are connected to form simple motifs


Simple combinations of a few secondary structure elements with a specific geometric arrangement which occur frequently in protein structures are called supersecondary structures or motif

The calcium-binding motif, EF-hand

EF Hand
Consists of two perpendicular 10 to 12 residue alpha helices with a 12-residue loop region between Form a single calcium-binding site (helix-loop-helix). Calcium ions interact with residues contained within the loop region. Each of the 12 residues in the loop region is important for calcium coordination. In most EF-hand proteins the residue at position 12 is a glutamate. The glutamate contributes both its side-chain oxygens for calcium coordination.

Calmodulin, recoverin : Regulatory proteins Calbindin, parvalbumin: Structural proteins

The hairpin beta-motif occurs frequently in protein structures

The Greek key motif is found in anti-parallel -sheets

Large polypeptide chains fold into several domains


Fundamental unit of tertiary structure DOMAIN Domain: polypeptide chain or a part of polypeptide chain that can independently fold into a stable tertiary structure Domains are also units of function

Tertiary structure refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds.

Quaternary structure
Proteins containing more than one polypeptide chain exhibit a fourth level of structural organization. Each polypeptide chain in such a protein is called a subunit. Quaternary structure refers to the spatial arrangement of subunits and the nature of their interactions. The simplest sort of quaternary structure is a dimer, consisting of two identical subunits.

Qaternary structure (higher order)

Complex Quaternary Structure. The coat of rhinovirus comprises 60 copies of each subunits

Protein structures can be divided into three main classes


Domain structures core is exclusively built from helices

Domain structures core comprises of antiparallel sheets, usually two sheets packed against each other / Domain structures made from combinations of -- motifs that form a predominantly parallel sheets surrounded by helices

Human plasma retinol binding protein. Retinol molecule vitamin A bound inside the barrel

Triosephosphate isomerase

Solving Protein Structures


Only 2 kinds of techniques allow one to get atomic resolution pictures of macromolecules X-ray Crystallography (first applied in 1961 - Kendrew & Perutz) NMR Spectroscopy (first applied in 1983 - Ernst & Wuthrich)

Structure Structure Structure

Function Mechanism Origins/Evolution

Structure-based Drug Design Solving the Protein Folding Problem

QHTAWCLTSEQHTAAVIWDCETPGKQNGAYQEDCA HHHHHHCCEEEEEEEEEEECCHHHHHHHCCCCCCC

First X-ray crystallographic structure Myoglobin (1958, Sir John Kendrew, MRC) Remarkable features: Complexity & Asymmetry

10

50 years since first protein structure determined (by X-ray crystallography)

Nobel prize - 1962

Myoglobin March 1958

Atomic resolution structures of biomolecules are stored at the Protein Data Bank

PDB contains 75000 structures mostly determined by X-ray crystallography and NMR. About 3-5 new structures per day

Using electrophoresis, Pauling showed that individuals with sickle cell disease had a modified form of Hb

Importance of Protein Structure

Hemoglobin A: Val-His-Leu-Thr-Pro-Glu-Glu-LysHemoglobin S: Val-His-Leu-Thr-Pro-Val-Glu-Lys-

sticky patch causes hemoglobin S to agglutinate (stick together) and form fibers which deform the red blood cell

Protein folding
Consider a small protein with 100 residues. Cyrus Levinthal calculated that, if each residue can assume three different conformations, the total number of structures would be 3100, which is equal to 5 1047. If it takes 10-13 s to convert one structure into another, the total search time would be 5 1047 10-13 s, which is equal to 5 1034 s, or 1.6 1027 years. Clearly, it would take much too long for even a small protein to fold properly by randomly trying out all possible conformations. Theenormous difference between calculated and actual folding times is called Levinthal's paradox.

Hydrophobic effect Conformational entropy Electrostatics Hydrogen bonding van der Waals interaction

Most important featureThe interior of proteins is hydrophobic ! The main driving force for folding water soluble globular protein molecules is to pack hydrophobic side chains into the interior of the molecule , thus creating a HYDROPHOBIC CORE and a HYDROPHILLIC SURFACE. Problem- How to create such a hydrophobic core from a protein chain ???

Classes of Proteins Based on structure and solubility, proteins can be grouped into three large classes:

Fibrous

Globular

Membrane

Protein Sequencing and Identification by Mass Spectrometry


Peptide Mass (D) 57 + 97 + 147 + 114 = 415

Peptide Mass (D)

without 57 + 97 + 147 + 114 18 = 397

Tandem Mass-Spectrometry

Protein-Protein Interaction Networks


Yeast ~6000 proteins, ~3 interactions per protein, i.e. ~>20,000 interactions. Humans ~100,000 interactions

Which two proteins will interact? AND, which will not? The ANSWER lies in the nature of the interacting surfaces

Nat. Biotechnol. 18, 12571261 (2000)

A-B, A-C forms poorly matched surfaces, few weak bonds are formed, broken apart by thermal motion A-D offers well matched surfaces, enough noncovalent bonds are formed to create a stable interface

Forces driving protein-protein interaction Long-range attractive interactions electrostatic steering

Short-range non-covalent forces:


Hydrophobic interactions van der Waals attraction Hydrogen bonds Ion pairs

Other factors:

Shape and charge complementarity


Secondary structure Amino acid composition