Principles of protein structure

Lecture series:
Blood:molecules and cells
Piet Gros

Protein structure
Physical interactions
type of interactions
characteristics of amino-acid residues
Role of water/solvent

What is the basis of protein folding?

Levels of structure: primary to quaternary
Protein structure visualization and analysis
Protein dynamics

FREE ENERGY !!!

Enthalpy: typically described in terms interactions
Entropy: order-disorder and importance of water

Types of interactions
Quantum chemical calculations not feasible for proteins!
Thus, interactions described by empirical terms

Covalent interactions:

Etotal
= E
Edihedral + Evanderwaals + Eelectrostatic
bond + Edihedral
angle + angles
Bonds,
bond-angles,

Non-covalent interactions:

Van der Waals interactions (Lennard-Jones potential)

Electrostatic interactions
(Coulomb interactions)
Hydrogen bonds
Dipolar interactions

Bond length energies for C-O bond length

Bond angle energies for N-C-O bond

Dihedral angles

The peptide bond usually adopts the trans conformation

Proline occurs relatively often in the Cis conformation

Main-chain conformation

Ramachandran plot

Side chain nomenclature

Preferred rotamers depend on the side chain

Non-covalent interactions
Zie Hfdstk 3 Intermoleculaire wisselwerking
Diktaat Fysische chemie 2, Prof. HNW Lekkerkerker e.a.
for physical chemical background on molecular interactions
- attraction and repulsion
- dipolar interactions
- dispersive interactions

Van der Waals interactions

I

II

III

E(r)

r
I:
II:
III:

repulsion from overlap of electron density

see I+III
overlap negligible, attraction due electric dipole interaction,
polarisation energy and dispersive interaction

Basis of Van der Waals attractive forces

An atom in isolation

An external electrostatic field produces polarization,

which causes a small dipole

The dipole from one atom causes an induce

dipole in the second
Now, the two atoms attract each other.

Van der Waals forces

Balance of attraction and repulsion

Lennard-Jones potential: strong distance dependence

Energy, (kcal/mol)

0.2
0.15

Lennard-Jones potential

0.1
0.05
0.0

Optimal distance: 3.8

-.05
-.1
-.15

van der Waals radius

in
C (aliphatic)
O
H
N
P
S

1.85
1.60
1.00
1.75
2.10
2.00

van der Waals well depth

in kcal/mol
0.12
0.20
0.02
0.16
0.20
0.20

Electrostatic interactions

Eelectrostatic

atom pairs ij

qi q j
4Rij

( i.e. charge generate an

electrostatic field )

Hydrogen bonding
Energy (kcal/mol)

Hydrogen bond potential

The Hydrogen bond: special case :

Strong bond: weak covalent bond
Short optimal distance (2.8 )

The molecules which have this extra bonding are:

Notice that in each of these molecules:

The hydrogen is attached directly to one of the most electronegative elements, causing the
hydrogen to acquire a significant amount of positive charge.
Each of the elements to which the hydrogen is attached is not only significantly negative,
but also has at least one "active" lone pair.
The involvement of the lone pairs causes a angular dependence of the hydrogen bonds!.

Water makes many hydrogen bonds

Water is oriented by hydrogen bonds

Effects of the surrounding solvent

H-bonding
Protein-protein vs. protein-water

Charged solutes shield electrostatic effect

Dielectric constant

Chaotropic solutes (de-)stabilize protein structure

Guanidium chloride, ureum,

Entropy
Order/disorder: water structure has an important
contribution!

Protein folding

Enthalpy & Entropy

non-covalent interactions
hydrophobic interaction (!?)
hydrogen bonds
ionic interactions

G ~ 5-15 kcal/mol
(about 3x a H-bond)

folded proteins more ordered:entropy less favourable

water on the surface of unfolded protein is more
ordered: folding favourable

A protein has multiple substates:

Substates of a folded protein

are accessed by dynamical
transitions

intermediate
folding states
folded protein

Characteristics of a folded protein

H-bonding donors and acceptors fulfilled
2nd structural elements present!

Hydrophobic on the inside

Polar and charged on outside
(when inside charge must be compensated)

Misfolding leads to fibril formation (prions)

Possibly, folded protein structures are kinetically
determined and fibril structures may be the
thermodynamically minimum configuration !

-helix: 3.613
3.6 residues per turn
rise of 5.4 per turn
(1.5 per residue)
dipole moment
amino-acid preference
(helical wheel)

Stryer

Stryer

Different types of tight turns

These conformations can be recognized by specific /

combination of subsequent residues (in a Ramachandran plot)

Nature of the amino-acid residues

Names+single letter codes

Aliphatic, Aromatic, Polar, Charged,
pKa
Hydrophobicity
Structural propensities

Stryer

The 20 amino acids

that occur naturally

Residue characteristics

Size:
G,A,T,V, W
Aliphatic:
A,V,L,I
Aromatic:
F,Y,W
Hydrophobic: A,V,L,I, but also F,P,W,C,Y,T,G and
K,R!
Polar:
N,Q,S,T,C but also Y,W
Charged:
D,E,H,K,R, but also Y,C depends on pH
Special:
G = flexible,
P = helix breaker,
C-C disulphide bonds depends redox potential
cytosol is reduced: -SH
ER and extracellular oxidized: S-S

Stryer

Structure prediction
From primary sequence to secondary and tertiary structure
Large number of methods: www.expasy.ch
Success rate for 2nd structure elements ~xx%
Information used:
Structural propensity: statistical preference for 2 nd structural element; e.g. Pro is
helix breaker, C-branched res. in -strands,
Hydropobicity: -helical wheel; alternation in -strands; trans-membrane segments;

Multiple alignments
Structural motifs
Threading thru known structures

CASP prediction competition

Tertiary structure - fold space

Databases with fold classification:
CATH: Class(C), Architecture(A), Topology(T)
and Homologous superfamily (H).
http://www.biochem.ucl.ac.uk/bsm/cath_new/
SCOP:Structural Classification of Proteins
http://scop.mrc-lmb.cam.ac.uk/scop/

Example SCOP
Protein: Hemoglobin, alpha-chain from Human (Homo sapiens)

Lineage:

1.Root: scop
2.Class: All alpha proteins
3.Fold: Globin-like
core: 6 helices; folded leaf, partly opened
4.Superfamily: Globin-like
5.Family: Globins
Heme-binding protein
6.Protein: Hemoglobin, alpha-chain
7.Species: Human (Homo sapiens)

plus a long list of related PDB files

Stryer

Stryer

Stryer

Stryer

Structures in the PDB

http://www.rcsb.org/pdb/

Structural genomics
Previous goals:
Completing fold space (a basis for homology
building)
Deriving function from structure

Current goals focus structural+functional

genomics
For example, TB-project,

Quaternary structure
Complex of multiple chains: e.g. 22 of hemoglobin
Not-quaternary but related:

multi-domain organisation
domain-domain interaction

A1 A2 A3

VWF:
C1r:

SCR1

SCR2

2050

SP

705
Part of C1qr2s2

C1r:
C2:

SCR1

SCR1

SCR2

SCR3

SCR2

VWA

SP

688
SP

752

2-Glycoprotein I
Membrane and protein adhesion molecule
Heavily glycosylated
only few of the glycan units present in crystal structure

Auto-antigen in Anti-Phospholipid Syndrome

Potential role in oxidative stress

II III IV V

protein
adhesion

membrane
adhesion

326

+-

Protein-ligand interaction

Salt-bridge, H-bonds, vdWaals int. = shape complementarity,

partially buried in the protein (entropy)

Binding: enthalpy & entropy

60
50

ResponseUnits

A
B
linear
peptide

40
30
20
10
0
0

C
D

peptideconcentration(M)

Binding to bactericidal antibody MN5C11G

Glossary
Covalent interactions:
bonds, bond-angle, dihedral angle

Non-covalent interactions:
vdWaals, electrostatic, dipole interaction

Enthalpy, entropy
hydrophobic interaction
folding dynamics

All natural residues and their characteristics

Primary, secondary, tertiary and quaternary structure:
Helices, -sheets, turns, motifs, domains

Sequence-structure-function