Biological Macromolecules
Chemistry and Chemical Biology
Rutgers University
Overview
• Bonds and Molecules
• Interactions in Biology
– Non-covalent:
• Hydrogen bonds, Hydrophobic interactions, Electrostatic
interactions
– Covalent:
• Disulfide bonds, Coordinate bonds
• Proteins
• Nucleic Acids
Bonds and Molecules
• Small Molecules and Macromolecules
• Properties of Single Bonds (Covalent)
– Chirality
– Configuration
– Conformation
Chirality
Molecular Chirality
Configuration
a-D-glucopyranose
b-D-glucopyranose
• To go from a-D-glucose to b-D-glucose a bond
has to be broken
L- and D- configurations of amino acids
L-Threonine
D-Threonine
Mirror plane
L-allo-Threonine
D-allo-Threonine
Conformation
•
•
•
•
Described in terms of torsion angles
Rotation around bond
No bonds broken
Minimize non bonded interactions
Positive & Negative Torsion Angles
(A) +Q: Clockwise rotation of front bond (about central bond) to eclipse the bond to the back
(B) -Q: Counter clockwise rotation of front bond to eclipse the bond to the back
From http://www.currentprotocols.com/protocol/nca01c
Torsion Angle Nomenclature
Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, p. 16.
Conformation Examples
Cyclohexanes
Pyranose
sugars
Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, pp. 249-250.
Non-covalent Interactions in Biology
• Non-covalent:
– Hydrogen bonds
– Hydrophobic interactions
– Electrostatic interactions
• Covalent:
– Disulfide bonds
– Coordinate bonds
Hydrogen bonding
Examples of Hydrogen Bonding
Water Hydrogen Bonding
Ice structure
Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 30.
Hydrophobic interactions
Clathrate hydrates
Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 179.
Electrostatic interactions
Example of electrostatic interaction
in PDB entry 1HSA (MHC complex)
Disulfide Bridges
Example of a disulfide bond in
PDB entry 1HSA (MHC complex)
Coordinate Bonding
N-ter
Example of a
Zinc Finger domain
From PDB entry 1ZAA
(ZIF268 protein)
C-ter
Proteins
Protein Building Blocks: Amino Acids
• Amino acid sequence
determines the 3D
structure of a protein
• 20 amino acids –
modifications do occur
post protein synthesis
• L- Amino acids in normal
proteins “corn crib”
Voet, Donald and Judith G.
Biochemistry.
John Wiley & Sons, 1990, p. 68.
From www.bachem.com
Amino Acids
Protein Building: Peptide Bonds
• Individual amino acids
form a polypeptide chain
• The polypeptide chain is
a component of a
hierarchy for describing
protein structure
• The chain has its own
set of attributes
Conformation of
the Polypeptide Chain
S
f
T
y
f
f
L
y
L
y
f
W
y
f
y
f
Q
• Omega (w): Rotation around the peptide
bond Cn – N(n+1). It is planar and is 180
under ideal conditions
• Phi (f): is the angle around N – Ca
• Psi (y): is the angle around Ca – C
w
y
T
• Values of f and y are constrained to
certain values based on steric clashes of
the R group.
• Ramachandran plot: Defines characteristic
patterns of torsion angles
Ramachandran Plot
• Allowed & disallowed
regions of f - y
• Exceptions:
• .
– Gly has no limitation
– Pro is constrained since its
side chain binds back to the
main chain
• The F-y values for
secondary structural
elements are clustered
Gray = allowed conformations. bA, antiparallel b sheet; bP, parallel b
sheet; bT, twisted b sheet (parallel or anti-parallel); a, right-handed a
helix; L, left-handed helix; 3, 310 helix; p, p helix.
Four Levels of Protein Structure
• Primary, 1o
– Amino acid sequence;
Covalent bonds
• Secondary, 2o
– Local conformation of
main-chain (polypeptide
backbone) atoms
(clustered F - Y angles);
non-covalent interactions
(H-bonds)
TPEEKSAVTALWGKV
Four Levels of Protein Structure
• Tertiary, 3o
– 3D arrangement of all atoms
in space (main-chain and
side-chain); non-covalent
interactions; covalent
interactions may also
contribute (e.g. S-S bonds)
b2
a2
a1
b2
b1
• Quaternary, 4o
– Interaction of subunit chains;
non-covalent interactions
Secondary Structure: Alpha Helices
• If N-terminus is at bottom,
then all peptide N-H bonds
point “down” and all peptide
C=O bonds point “up”.
• C=O(i) is H-bonded to NH(i+4).
• Features:
– 3.6 residues per turn
– Rise/residue = 1.5 Å
– Rise/turn = 5.4Å
a Helix
• R-groups in a-helices:
– extend radially from the core,
– shown in helical wheel diagram.
– Can have varied distributions
Polar
Hydrophobic
Amphipathic
Secondary Structure: b Sheet
• Stabilized by H-bonds
between N-H & C=O
from adjacent
stretches of strands
• Peptide chains are
fully extended pleated
shape because
adjacent peptides
groups can’t be
coplanar.
Beta Sheets
Antiparallel beta sheet
Parallel beta sheet
Optimum H-bonds; more stable
Not optimum H-bonds; less stable
The Beta Turn
AA2
AA1
AA3
AA4
• H-bond between N-H(i)
and C=O(i+3)
• Beta-turns can have 2
different conformations
Motifs
• Motif (structural motif) :
Arrangement of secondary
structural elements
• May not have same/similar
biochemical function
• May also be called supersecondary structure
Helix-turn-helix motif
PDB ID 1lmb
Greek-key motif
PDB ID 3ix0
• Note: Sequence motifs are
recognizable aa sequence with a
biochemical function
b-a-b motif
PDB ID 2gcf
Examples of Tertiary Interactions
• Charge based interactions
– 62R:163E 1
– 55E:170R
• Hydrophobic interactions 2
– 189V
– 201L
– 213I
– 215L
– 266L
• Disulfide bond
– 203C:259C 3
domains
Domains
• Collection of several secondary structural
elements and/or motifs
• Tertiary structure
• Usually has a hydrophobic core
• May be a complete protein or part of a
protein
• May be stabilized by covalent interactions
(S-S bonds, coordinate covalent bonds)
• Types: alpha, beta, alpha/beta (LevittChothia classification)
Protein Domain Examples
Globin fold (Myoglobin)
PDB ID 1ajg
TIM Barrel
PDB ID 1tim
Jelly roll
PDB ID 1k5j
Domain Classifications
• Sequence based
– PFAM: protein families, represented by multiple
sequence alignments
• Structure based
– SCOP: Structural Classification of Proteins
– CATH: Class(C), Architecture(A), Topology(T),
Homologous superfamily (H)
• Class(C)
derived from secondary
structure content is assigned
automatically
• Architecture(A)
describes the gross
orientation of secondary
structures, independent of
connectivity.
• Topology(T)
clusters structures according
to their topological
connections and numbers of
secondary structures
[ http://www.biochem.ucl.ac.uk/bsm/cath_new/ ]
Quaternary Structure
• Composed of 2 or
more polypeptide
chains
• Intermolecular
interactions may be
non-covalent or
covalent
• Inappropriate
interactions in
disease (sickle cell
hemoglobin mutant
E6V in b2)
References
• "Introduction to protein structure", Brandon and
Tooze, 3, 21, 1999.
• Voet, Donald and Judith G. Biochemistry. John
Wiley & Sons, 1990
• “Protein Structure and Function”, Petsko and
Ringe, New Science Press Ltd., 2004
Nucleic Acid Structures
Base
Sugar
Phosphate
Building Blocks in NucleotidesBases
• Bases
– Purines and Pyrimidines
– Bases in DNA (dA, dT,
dG, dC)
– Bases in RNA (A, U, G,
C)
• Sugars
– DNA has deoxy ribose
sugar
– RNA has ribose sugar
C5’
C5’
C5’
P
• Phosphate
deoxy-ribose
Phosphate
ribose
Sugars
Watson Crick Base Pairs
Geometry of A:T and G:C
base pairs are isosteric
Tautomeric structures
• Keto vs enol
• Different hydrogen
bonding patterns
Diversity of hydrogen bonding
geometries
Base Morphology: Propeller twist
Base Morphology: Base pair twist
• Looking down helix axis
• 36 degree base pair twist
in B-DNA
B-DNA structure in 424D
Backbone conformation
Anti vs. syn
Anti conformation
Syn conformation
Change in sugar conformation
affects the backbone
Ribose ring is never flat
A DNA vs B DNA
A-DNA
B-DNA
B DNA
• .
Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.
A DNA
Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.
Z DNA
• Left handed
• Very deep minor
groove
• Major groove on
outside
Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.
G pairing in quadruplex
Top view 1L1H
Side view 1L1H
Close-up of G-pairing
RNA Structures: tRNA
Secondary and Tertiary Structures
RNA
• Double and single stranded
• Double helix has A-form structure
• Single stranded forms globular structure
406D RNA double helix
1NYI Hammerhead ribozyme
387D RNA Pseudoknot
References
• Saenger, Wolfram. Principles of Nucleic
Acid Structure. Springer-Verlag New York
Inc., 1984, pp. 109, 113.
• Neidle, Stephen. Nucleic Acid Structure
and Recognition. Oxford University Press,
2002, pp. 18, 21-22, 34, 36, 68, 90, 165166.
• Voet, Donald and Judith G. Biochemistry.
John Wiley & Sons, 1990, pp. 792, 797,
807-809