Molecular Interactions
I.
INTRODUCTION
A. Interactions between macromoleules is the rule rather than the exception
1. Examples
a) DNA and histones
b) Viral nucleic acid packaged in protein capsid
c) Tendons are formed by interactions between proteins
d) Membranes are composed of lipids and proteins
II.COLLAGEN
A. Most abundant protein in mammals
1. Makes up a quarter of all protein
a) Tendons, cartilage, bone, skin, blood vessels
2. Fiber with great tensile strength
B. Made by fibroblasts
1. Secreted as procollagen
a) Procollagen (0.4 nm)
2. Organized into higher levels
a) Tropocollagen
(1) Three -helices wrapped in a triple helix
b) Collagen fibers (1 - 10 m)
c) Tendons, cartilage, bone, etc (macroscopic)
C. Primary structure
1. ~1000 amino acids
2. ~1/3 glycine
a) Every third amino acid
(1) Usually accounts for only 7.5% of amino acids in other proteins
3. ~1/4 proline
a) Or hydroxyproline
(1) Not found in other proteins
4. Many hydroxylated lysines (hydroxylysine)
a) Hydroxylation involves vitamin C
(1) Scurvy (a result of vitamin C deficiency) results in weakened collagen
5. Many glycine - proline - hydroxyproline repeats
a) Repeats are unusual in other proteins
D. Secondary structure
1. Proline's N of the peptide group is attached to the side chain
a) Bond is less flexible
b) Causes chain to be extended
(1) 3.3 residues per turn instead of 3.6 normally found in an -helix
E. Tertiary Structure
1. Very little
2. Extended configuration inhibits intrastrand interactions
F. Quantenary Structure
1. Extended structure causes amino acid side chains to be more exposed
a) Individual strands interact by means of interstrand H-bonds (between
peptide groups)
2. Forms a triple stranded helix
3. Glycine on inside (internal)
a) Glycine's hydrogen side chain is the only one that fits
b) Proline other amino acid side chains are external (sticking out from the
helix)
G. Collagen Fibers
1. Three strands of collagen form tropocollagen
2. Tropocollagen associates in a quarter staggered array
a) Banded when stained
(1) Phosphotungstic acid stains positively charged amino acids
(2) Uranyl acetate stains negatively charged amino acids
b) Bands are due to clusters of positively and negatively charged amio acids
(1) Ionic bonds cause tropocollagen molecules to associate
(2) Individual tropocollagen molecules do not fold in on themselves because of
extended structure
3. Gaps filled with hydroxyapetite
a) Ca10(PO4)6OH2
4. Hydroxyproline and hydroxylysine
a) Engaged in covalent cross-links
(1) Within a tropocollagen
(2) Between tropocollagen
b) Cross-links are continued throughout life
(1) Makes bone more brittle
(2) Makes skin less elastic
III.PROTEINS
THAT RECOGNIZE SPECIFIC BASE SEQUENCES
A. Types
1. Regulatory proteins
2. Restriction endonucleases
3. Polymerases
B. Cro protein
1. General
a) From Escherichia coli phage 
(1) Small (66 residues) basic protein
(2) Binds to 17 bp region of phage  DNA
b) Secondary structure
(1) 3 strands of antiparallel -sheets
(a) 2 - 6
(b) 39 - 45
(c) 48 - 55
(2) 3 -helices
(a) 7 - 14
(b) 15 - 23
(c) 27 - 36
c) Areas of DNA attachment
(1) Dimethyl sulfate
(a) Methylates
(i) N-7 G
(ii) N-3A
(a) Both purines
(b) Those not methylated in contact with Cro
(2) Phosphate contacts
(a) Briefly ethylated DNA
(b) Differences between ones Cro did and did not bind determined
(3) Contact points are
(a) On one side of the molecule
(b) Located on both strands
(c) In wide groove of DNA
(d) Contact points are nearly symmetrical
d) Structure of Cro
(1) Homodimer
(2) Symmetrical
(3) 34 Å between 3-helices
(a) Spacing required to fit into successive major grooves from one-side of a
DNA molecule
e) Complex
(1) 3 fits into major groove
(a) Hydrogen bonds between protein and DNA
(b) Provides specificity of binding
(2) Other amino acid side chains bind to phosphate
(a) Ionic bonds
(b) Provides strength of interactions
(3) Binds to DNA (phosphate) and slides to it settles at proper base pair sequence
f) Common factors with other DNA binding proteins
(1) Symmetric dimers
(2) At least 2  helices spaced 34 å apart (inclined 32)
(a) Allows binding to major grooves
(b) -sheets are not common
(3) Amino acid side chains on surface of  helices are capable of H-bonding with
particular groups on the bases
(4) 3 helix determines specificity
(a)  helices in histones also bind DNA, but there is no specificity
(b) Amino acid sequence of 3 helices varies for recognition of different
sequences
(i) Some nucleotide sequences may be recognized by different amino
acid sequences
g) Hybrid proteins
(1) EcoR1 and Klenow fragment of DNA polymerase 1
(2) DNA polymerase 1
(3) Not a dimer
(i) 600 residues
(ii) 19  helices
(a) Two  resemble 2 and 3
(iii) 13  sheets
(b) Slides down DNA, but does not bind to one sequence
IV.TOBACCO
MOSAIC VIRUS
A. Structure
1. 300 nm
2. 2130 identical subunits
a) Packed in a helical array
b) Each protein subunit interacts with three nucleotides
3. 6390 nucleotide ssRNA
B. Assembly
1. Proteins spontaneously form a 2 layer disc
a) 17 protein subunits per disk
b) Intermediate form
2. They slide over each other to form a two-turn helix
a) Lock and washer
3. Discs recognize a specific TMV RNA sequence
a) Add few disc, degrade RNA, remove protein
b) 65 nucleotides
(1) Hair pin loop
(2) 5300 from 5’ end (gets shorter)
(3) 1000 from 3’ end (stays constant)
(a) Two tails
c) Double layered disc slips over the loop
(1) As it converts to the locked washer, the 5’ end is pulled up to maintain the loop
(2) Next double layered disc slips over, etc.
(3) RNA loops as discs are added
d) 3’ tail is coated by unknown mechanisms