Perspectives of Structure-Sequence Dependent
Stability of Collagen and Interaction of
Polyphenol Molecules with Collagen
V. Subramanian
Chemical Laboratory
Central Leather Research Institute
Chennai
Introduction
 Collagen is an extremely important protein, which
provides mechanical strength and structural
integrity to connective tissues
 Nineteen different collagen types identified till date
 The identifying motif of the collagen is triple helix
 Prof Ramachandran and co-workers and Rich and
Crick
 The Gly-X-Y is the general repeating sequence of
the collagen (33% of Gly)
 Mutations in collagen chain can render the fibrils
unstable
Triple Helix
 The collagen triple helix constitutes the major motif in fibril
forming collagen and also occur as a domain in non-fibrillar
collagens
 Hydrogen bonding and presence of high content of imino acids
provide stability to the three dimensional structure of collagen
 The role of water mediated hydrogen bonding and hydration
also play a crucial role in the stability of collagen
 Recent experimental studies revealed that the presence of Arg
in the Y position provides equal stability when compared to
Gly-Pro-Hyp
 The destabilizing nature of Asp in the Y position is also evident
from the experimental studies
 Therefore assessment of propensity of various amino acids to
form collagen like peptides is an important area of research
activity
Collagen Structure: An Indian Origin
 Single Vs two hydrogen bond(s)
 If X and Y positions are imino acids, there is no
possibility of forming two hydrogen bonds
 The incorporation of other amino acids
provides a possibility of readdressing this
question
Stabilizing
Inter-strand
H-bonds
Collagen Triple Helix
Propensity of Various Amino Acids to Form
Collagen Like Motif: Guest Host Approach
 Propensity of various amino acids to form alpha
helix and beta sheet have been addressed
 Host-Guest peptide approach has been used to
estimate the propensity
 The presence of various amino acids not only
influences the three dimensional structure but also
the stability of collagen
 The amino acid propensity-stability-function is an
important area of research in molecular biophysics
 Several experimental studies have been carried out
on model collagen-like peptides to establish the
propensity of various amino acids to form collagen
Triple Helix Propensity Scale
 Circular dichrosim Spectroscopy has been used to develop
triple helix propensity of various amino acids
 The molar elipticity was monitored at 225nm while sample
temperature was increased from 0 to 800 C
 The melting curves were used to calculate fraction of folded
states
 Fraction folded has been used to compute vant Hoff
enthalpies and free energy
 These information provides experimental basis for
predicting relative stabilities of various amino acids to form
collagen like structure
 Propensity scales will be used to compare the results
obtained from modeling and simulations
0
 (T )   M (T )
F (T ) 
 T (T )   M (T )
K (T ) 

3c 1  F (T )
F (T )
2
0
3

 H
K (T )  exp 
 RT
 T   3c02  
  1  ln   
 Tm   4  
Unraveling the Stability of Collagen: Experimental
Studies by Brodsky and Co-workers
 Host-Guest approach has been used to introduce new sequences in
the general repeating Gly-Pro-Hyp sequences
 Parameters such as
 melting temperature
 thermodynamics parameters from melting studies
 G of stabilization
of the host-guest collagen-like peptides have been studied to identify
the influence of amino-acids towards the stability of collagen
Thermodynamics parameters for the Guest Host peptides
Biochemistry, 1996, 32, 10262.
Propensity data from Brodsky work
Melting Temperature & Thermodynamic parameters for
the Guest Host peptides in Y position
Biochemistry, 2000, 39, 14960.
Melting Temperature & Thermodynamic parameters for
the Guest Host peptides in X position
Collagen in Diseases
 Mutation in collagen genes COL1A1 and COL1A2 leads
to Osteogenesis Imperfecta (OI), a brittle bone disease
 A point mutation in one of types collagen genes can
cause disease
 One of the main cause for OI is GlyAla mutation
 Glycine substitutions to another amino acid more severe
than mutations of X or Y in Gly - X - Y triplet.
 Understanding the stability of collagen upon mutation
becomes necessary
 Since collagen is a large protein, it is difficult to study the
influence of amino acids
 Various attempts have been made to probe the effect of
mutation in model collagen-like peptide sequences
Collagen in Diseases
 Mutations in collagen leads to Osteogenesis
Imperfecta (Type –I), Chondrodysplasis (type II),
Ehlers-Danlos syndrome (type III), Alport syndrome
(type IV), Bethlem myopathy (type VI) etc
 Mutation in collagen genes COL1A1 and COL1A2
leads to Osteogenesis Imperfecta (OI), a brittle bone
disease
 A point mutation in one of type I collagen genes can
cause disease
 One of the main causes for OI is GlyAla mutation
 Glycine substitutions to another amino acid is more
severe than mutations of X or Y in Gly - X - Y triplet
Understanding the stability of collagen upon mutation
becomes necessary
Collagen mimics and Biomaterial
applications
 Various physical and chemical properties make collagen
as a versatile material for biomaterial applications
 Studies on Collagen mimetics have been made to
understand the strength of triple helix and for their
application in biomaterials
 In collagen mimetics, a variety of unnatural amino acids
are incorporated in X and Y positions
 K. N. Ganesh* and his coworkers have used 4 amino
proline containing collagen like sequences
 Murray Goodmann$ and his group made an attempt to
template assembling of collagen like peptides using
conformationally constrained organic molecule
*JACS, 1996, 118, 5156
$JACS, 2001, 123, 2079
Frequency of Occurrence of Selected
Triplets in Collagen
Propensity of Various Amino Acids to Form
Collagen Like Motif
 The propensity of various amino acids to form alpha
helix and beta sheet have already been established
 Host-Guest peptide approach has been used to
estimate the propensity
 The presence of various amino acids not only
influences the three dimensional structure but also
the stability of collagen
 The amino acid propensity-stability-function is an
important area of research in molecular biophysics
 Several experimental studies have been carried out
on model collagen-like peptides to establish the
propensity of various amino acids to form collagen
Issues addressed
 To determine the stability of collagen upon
substitution of Gly-Pro-Hyp by other collagen-like
triplets
 To develop the propensity scale for various amino
acids to form collagen-like peptides based on free
energy of mutation
 To probe the interaction between model collagen
like peptides with polyphenols
Methodology
 Ab initio and DFT calculations have been performed
on collagen like triplets in both collagen and extended
conformation
 Free energy of solvation for these triplets have been
computed for both conformations using Polarizable
Continuum Method
 Free energy of solvation has been used to compute the
stability and amino acid propensity
 The stability of these peptides have also been analysed
by calculation of hardness
 Free energy of various triplets have also been
computed using classical molecular dynamics
simulations
 Using these values free energy change has been
quantified
Model Collagen Triplets for Ab initio and DFT
calculations
Gly-Pro-Hyp Extended
conformation
Gly-Pro-Hyp collagenlike conformation
Superimposed structures
of Gly-Pro-Hyp in both
conformations
Relative Energy of Proline Containing Triplets
Relative Energy of Hyp Containing Triplets
Relative Energy of Triplets without Imino acids
Important Observations
 The triplets containing proline or hydroxy proline
are more stable in collagen-like conformation
 Proline sterically restricts the N-C rotation and it
has limited values of , – 63 ±15 degrees
 Hence, proline can not be found in other known
major protein motif
 The
dihedral
angle
corresponding
to
conformational energy minima for proline has been
found to be –75 and 145o (, )
 It can stabilize secondary structure of protein only
when the allowed values of all other amino acids
coincide with that of proline
Important Observations
………Contnd.
 It is evident from the relative energy that Gly-Gly-Hyp
does not stable in collagen like conformation
 Recent experimental evidence confirms that glycine in the
second position destabilizes the collagen triple helix
 Solvation drastically alters the relative energy
 Proper ordering of the stability of various triplets needs
geometry optimization in solvent media
Free Energy Solvation
Important Observations
 Solvation free energy of collagen-like sequences
indicates that the triplets in collagen-like
conformation can be hydrated better than its
extended counterpart
 The presence of polar and non-polar residues in the
sequence drastically influences the solvation
 Specifically Arg either in second or third position
influences the solvation
 Arg stabilizes the collagen-like sequence similar to
stability provided by Hyp in the Y position
Free Energy Cycle
1
3
2
4
Assessment of Stability Using G
 The propensity to form collagen-like sequence has
been calculated using Gly-Pro-Hyp as reference
 The calculated G ranges from 0.0 to 15.8
kcal/mol
 The change in the free energy of Gly-Pro-Pro and
Gly-Pro-Flp is close to Gly-Pro-Hyp
 The most stable sequence is Gly-Pro-Hyp
 The general trend correlates well with the
experimental values derived from melting
temperature studies on model systems
Triplets Involved in the Stability of Collagen: A
Propensity Scale
18
16
14
12
10
8
6
4
2
0
Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- Gly- GlyPro- Pro- Pro- Hyp- Phe- Gly- Leu- Glu- Pro- Ala- Pro- Ser- Pro- Glu- Pro- Pro- Pro- Pro- Pro- Pro- Glu- Ala- Asp- Pro- Ala- Ala- Asp- LysHyp Flp Pro Hyp Hyp Hyp Hyp Hyp Glu Hyp Val Hyp Ala Arg Arg Lys Ile Met Asp Ser Ala Asp Arg Thr Arg Lys Ala Asp
A Propensity Scale
-helix
b-sheet
Collagen
b-turn
Chemical Hardness
 Global hardness of various triplets in
collagen-like and extended conformation
has been calculated
 It interesting to note that the chemical
hardness values are more for the triplets in
collagen-like conformation than extended
conformation
 Experimentally, Asp in the triplet does not
favor collagen folding
 Chemical hardness for Gly-Pro-Asp is
observed to be less compared to the other
sequences
Important Observations
 B3LYP/6-31 G* level of theory predicted that collagen-like
conformation of the Gly-Pro-Hyp is stable than the
extended conformation by 0.46 kJ/mol
 Hardness of triplets of sequences Gly-X-Y (without Hyp
and Pro) is lower than the triplets containing Pro and Hyp
residues
Emerging Roles of Computational Techniques in
Tanning Theory
 Computer model of bovine type I collagen has
been simulated
 Early report of molecular modeling of tanning
processes has been made
 Model peptides for collagen has been selected and
interactions with various tanning materials
simulated using force field as well as Density
Functional Theoretical methods
 Binding energies for various interactions of
collagen like peptide with tannin molecules have
been estimated
Computer Simulation of
Collagen –like Peptide-Tannin Interaction
Collagen -Catechin
Collagen -Epicatechin
Collagen –Gallic Acid
Collagen -Quercetin
Interaction of gallic acid collagen like peptides
Gallic Acid
 Gallic acid is a good anti-oxidant present in many plant sources
 Gallic acid has been shown to selectively induce cell death in
cancerous cell lines by binding to specific receptors or enzymes
 Gallic acid finds major role in stabilization of collagen in
tanning process of leather making
 Collagen is an important and abundant connective tissue protein
in animal kingdom
 Collagen assemblies are stabilized by covalent and non-covalent
interactions
 A fundamental understanding on the interaction of gallic acid with
collagen is important to unravel the nature of interactions that are
required for the stabilization of collagen matrix
 Theoretical calculations can be used for the determination and
quantification of such interactions
 In this view present investigation focuses on determining the
interactions of different dipeptides with gallic acid
 Such a study can not only be correlated to stabilization process
involved in collagen but also will lead to the advancement on the
knowledge of peptide-ligand interaction
Computational details
 Three classical dipeptides of amino acids glutamic acid,
lysine and serine chosen for the interaction studies with
gallic acid
 Dipeptides imposed with the  and  corresponding to the
angles of collagen
 Dipeptides and gallic acid built and energy minimized
using modules available in Insight II(MSI, USA)
 Four functional sites namely 3 OH groups and one COOH
group present in the gallic acid identified to have the
potential to interact with the side chain groups of the
dipeptide
 The geometry of the complexes optimized by a semiempirical PM3 method using Gaussian98 suite of programs
 Energy of the complex calculated using both
Hartree Fock (HF) and DFT based B3LYP
methods using 3-21G* & 6-31G* basis sets
employing Gaussian 98w suite of programs
 The interaction energy (VINT) calculated
using supermolecule approach
VINT = TEcomplex – [ TEdipeptide + TEgallic
acid]
Binding Energy (VBE) is, VBE = - VINT
 Molecular electrostatic potentials (MESP) are useful in
understanding the weak and non-covalent interactions.
The electrostatic potential V(r) is defined as
V (r ) 
ZA
 (r ' )dr '

r  RA
r  r'
ZA is the charge on nucleus A located at RA, and (r') is
the electron density at a point r
 MESP features of peptide-gallic acid complex have
been studied by BLYP/DN using DMOL implemented
in Cerius2
 Molecular Dynamic (MD) calculations have been done
for one of the complexes, to see the time evolution of the
hydrogen-bonded complex. A time step of 1fs has been
chosen and the MD simulations have been performed
for 600 ps including an equilibration period of 100 ps
Discussion
 The functional groups para-OH, two meta-OH and COOH of
gallic acid have been assumed to act as a hydrogen bond
donor/acceptor for different side chain groups of amino acids in
dipeptide
 Most of the complexes have exhibited hydrogen bonding in the
complexes consisting of dipeptides-gallic acid
 Complexes have exhibited binding energies in the range of 4 –
18 kcal/mol
 Complexes of glutamic acid dipeptide with gallic acid have all
exhibited hydrogen bonding with high binding energies
 Some of the complexes of gallic acid with serine
and lysine dipeptide have also exhibited hydrogen
bonding
 The interaction with COOH group of gallic and
side chain COOH group of glutamic acid exhibited
the maximum binding energy
 All complexes calculated by HF methods predicted
lower binding energies when compared to the
binding energies predicted from DFT methods
 Molecular electrostatic potential estimation of
various complexes provided clues on the
involvement of the electrostatics involved in the
interaction process
Interaction energies of different sites of gallic acid
with different dipeptides calculated using Density
Functional Theory (B3LYP) with basis set 3-21G*
and 6-31G*
Binding energies of gallic acid – dipeptide complex (kcal/mol)
m1 – OH (C1)
p – OH (C2)
m2 – OH (C3)
COOH (C4)
321G*
631G*
321G*
631G*
321G*
631G*
321G*
631G*
Glutamic
Acid
10.29
8.08
7.06
5.06
11.19
8.98
18.18
15.1
Lysine
5.51
3.75
11.65
9.51
8.97
6.53
14.51
12.18
Serine
7.7
6.32
10.96
10
6.23
5.1
12.92
10.19
Dipeptide
Interaction energies of different sites of gallic acid with
different dipeptides calculated using Hartree Fock (HF)
method with basis set 3-21G* and 6-31G*
Binding energies of gallic acid dipeptide complex (kcal/mol)
Dipeptide
m1 – OH (C1)
p – OH (C2)
m2 – OH (C3)
COOH (C4)
321G*
631G*
321G*
631G*
321G*
631G*
321G*
6-31G*
Glutamic
Acid
8.67
6.0
6.12
3.85
9.3
6.7
16.86
13.39
Lysine
3.55
–3.25
11.57
9.15
7.95
5.22
12.6
10.33
Serine
7.28
5.91
10.65
9.34
6.02
4.39
12.59
9.46
Hydrogen Bonded Complexes
of Glutamic acid Dipeptide
and Gallic acid
C2
C2
C3
C4
Hydrogen Bonded Complexes of Lysine
Dipeptide and Gallic acid
C4
C2
Hydrogen Bonded Complex of Serine
Dipeptide and Gallic acid
-ve MESP of serine gallic complex (C1)
-ve MESP of glutamic-gallic complex (C4)
-ve MESP of lysine gallic complex (C2)
 The functional groups para-OH, two meta-OH and
COOH of gallic acid have been assumed to act as a
hydrogen bond donor/acceptor for different side chain
groups of amino acids in dipeptide
 Most of the complexes have exhibited hydrogen
bonding in the complexes consisting of dipeptidesgallic acid
 Complexes have exhibited binding energies in the
range of 4 – 18 kcal/mol
 Complexes of glutamic acid dipeptide with gallic acid
have all exhibited hydrogen bonding with high
binding energies
Collagen-like Peptide Sequence
 Difficult to handle large systems like collagen
molecule for molecular simulation calculations
 Interaction studies can be carried by building
collagen like peptide sequence maintaining the
uniqueness of collagen
 A 9-mer sequence Ace-Gly-Pro-Hyp-Gly-AlaSer-Gly-Glu-Arg-Nme is built based on the
repeatability of the sequences and on the
presence of amino acids in the actual collagen
molecule by imposing  and  constraints
based on G N Ramachandran plot
Interaction of Polyphenolics with
Collagen-like Peptide Sequence
 Peptide sequence and polyphenolic molecules minimized using
CVFF(Consistence Valence Force Field)
 The polyphenolic molecules placed near the different sites of the
peptide sequence and minimized
 The binding energy of the molecules with the peptide sequence
calculated based on the equation,
EB   E polyphenolics  Esequence   Ecomplex
EB - Binding Energy (kcal/mol)
Epolyphenolics = Total energy of the minimized structure of
polyphenolic molecules (kcal/mol)
Esequence
= Total energy of the minimized structure of
collagen-like peptide sequence (kcal/mol)
Interaction of Polyphenolics with
Collagen-like Peptide Sequence
Hydrogen bonded complex of Gallic acid with Serine residue
of collagen like peptide (Binding Energy = 8 kcal/mol )
Hydrogen bonded Complex of Catechin with
Peptide (Binding Energy = 18 kcal/mol )
Complex of Quercetin with collagen like
peptide (Binding Energy = 12 kcal/mol )
Molecular Electrostatic Potential Surface (MESP) of Gallic
acid–Collagen-like Peptide Complex
Positive electrostatic potential (0.7)
surface of the complex of gallic acid
with Glutamic acid residue of the
peptide sequence
Negative electrostatic potential (-0.01)
surface of the complex of gallic acid
with Glutamic acid residue of the
peptide sequence
Binding Energies of Polyphenol-Collagen-like Peptide
Complexes
Complexes
Binding Energies (kcal/mol)
Catechin
Quercetin
Gallic acid
1
19.10.2
13.70.2
8.20.1
2
16.40.1
16.20.2
7.10.1
3
15.60.2
12.20.1
6.10.2
[1]– Polyphenolic molecule interacted around the serine and glutamic acid residue of the
collagen-like peptide sequence.
[2]– Polyphenolic molecule interacted around the arginine residue of the model collagen-like
peptide sequence.
[3] –Polyphenolic molecule interacted around the hydroxyproline residue of the model
collagen-like peptide sequence.
Lessons from Molecular Modeling Studies
 Molecular modeling studies have provided
a basis to identify the interaction process
involved in tanning
 Catechin exhibited stronger binding, as
compared to other polyphenolics chosen
for the study
 Many of the complexes exhibited hydrogen
bonding and some exhibited electrostatic
and weak interactions
 MESP has revealed a lock and key type of
electrostatic interactions involved in the
stabilization of gallic acid and collagen-like
peptide complex
Geometrical Issues in binding small
molecules by collagen; A Prospective
Analysis
Computational Details
 Four representative polyphenol molecules viz., gallic
acid,
catechin,
epigallocatechingallate
and
pentagalloylglucose chosen for interaction studies
 24-mer collagen triple helix corresponding to residues
193 to 216 (21 and 12 chains) of the native Type I
collagen is constructed using the GENCOLLAGEN
package
 Following is the amino acid sequence of triple helix,
[Gly-Glu-Hyp-Gly-Pro-Hyp-Gly-Pro-Ala-Gly-Ala-LysGly-Pro-Ala-Gly-Asn-Hyp-Gly-Ala-Asp-Gly-Gln-Hyp]
1
[Gly-Glu-Val-Gly-Leu-Hyp-Gly-Leu-Ser-Gly-Pro-ValGly-Pro-Hyp-Gly-Asn-Ala-Gly-Pro-Asn-Gly-Leu-Hyp]
2
 The 24-mer triple helix and polyphenols
are minimized using CVFF with a
dielectric constant of 4.0
 Collagen - an inside out protein
 Side chain hydroxyl group of the amino
acids, serine and hydroxyproline, carboxyl
group of aspartic acid, amino group of
lysine and amide group of aspargine are
potential interacting sites for formation of
hydrogen bonds with polyphenols
Energy minimized structures of polyphenols
Catechin
Epigallo Catechin Gallate
Vegetable
Tannins
Penta
galloylglucose
Gallic acid
Energy minimized structure of 24-mer collagen triple
helix
Complex between aspargine of T.Helix and gallic acid
Complex between aspartic acid of T.Helix and
catechin
Complex between lysine of T.Helix and
epigallocatechingallate
Complex between aspargine of T.Helix and
pentagalloylglucose
Binding energies different complexes between
polyphenols and triple helix
Binding Energy (Kcal/mol)
Binding Sites in
triple helix
Catechin (Cat)
Epigallocatechi
ngallate
(EGCG)
Pentagalloyl
glucose (PGG)
16.5
22.5
35.2
56.6
6th residue Hyp
of A-chain (α1)
14.5
20.8
34.5
48.4
12th residue Lys
of B-chain (α1)
19.2
23.8
37.9
41.1
21st residue Asp
of A-chain (α1)
18.4
20.0
38.2
59.8
17th residue Asn
of C-chain (α2)
14.1
23.7
34.3
52.8
Gallic acid
(Gal)
9th residue Ser of
C-chain (α2)
Hydrogen bonds of complexes; their length and angle
Gallic acid (Gal)
Interaction Site
H-bond
9th residue Ser of Cchain (α2)
SerC9-(Cα)-C-O…H(3)O-Gal-
Pentagalloylglucose (PGG)
Bond
Dist Å
3.02
Bond
Angle
H-bond
Bond
Dist Å
Bond
angle
141
HypC15-(Cα)-O-H…O(19)-PGG
AsnA17-N-H…O(19)-PGG
AlaA15C=O…H(20)-PGG
SerC9-(Cα)-C-O…H(10)O- PGG
2.84
3.17
2.76
2.93
177
156
156
121
3.04
2.88
2.96
3.08
3.17
163
139
131
157
149
6th residue Hyp of Achain (α1)
AspB21C=O…H(3)O-Gal
2.97
138
GluB2-(Cα)-C-O-H…O(15)-PGG
GluB2-(Cα)-C-O…H(24)-PGG
HypB3C=O…H(23)-PGG
HypB3C=O…H(18)-PGG
LeuC5-N-H…O(12)-PGG
12th residue Lys of Bchain (α1)
LysB12-(Cα )N-H…O(2)- Gal
3.28
126
HypA18-(Cα)-O-H…O(3)-PGG
AsnB17-(Cα)-N-H…O(2)O-PGG
3.09
3.12
122
141
21st residue Asp of Achain (α1)
AspB21-(Cα)-O-H…O(3)-Gal
HypB18-C=O…H(6)O-Gal
2.89
2.91
128
147
AspA21-N-H…O(9)-PGG
GlyA19C=O…H(13)O-PGG
2.96
2.83
164
174
17th residue Asn of Cchain (α2)
AsnA17-(Cα)-C=O…H(3)O-Gal
2.84
151
AsnB17-(Cα)-C=O…H(8)O-PGG
HypA18C=O…H(4)O-PGG
GlyA16N…H(3)O-PGG
3.27
2.9
3.42
159
140
161
Catechin (Cat)
Interaction Site
Epigallocatechingallate (EGCG)
H-bond
Bond
dist Å
Bond
Angle
H-bond
Bond
dist Å
Bond
angle
9th residue Ser of Cchain (α2)
SerC9-(Cα)-O-H…O(2)-Cat
3.04
161
LysA12C=O…H(9)O- EGCG
SerC9-C=O…H(3)O- EGCG
2.82
2.79
148
132
6th residue Hyp of Achain (α1)
HypA6-(Cα)-O-H…O(1)-Cat
AlaB9-N…H(12)O-Cat
3.02
3.18
127
137
ProB8-N… H(13)O- EGCG
3.25
142
12th residue Lys of Bchain (α1)
LysB12C=O…H(11)O-Cat
3.1
126
LysB12-(Cα)-N-H…O(2)- EGCG
3.41
150
21st residue Asp of Achain (α1)
AspA21-(Cα)-C-O-H…O(4)-Cat
AlaB20-NH…O(2)-Cat
GlnA23-(Cα)-N-H…O(6)-Cat
3.08
3.22
3.24
150
133
164
17th residue Asn of Cchain (α2)
GlyA16C=O…H(14)O-Cat
AsnA17-(Cα)-C=O…H(11)O-Cat
3.00
2.92
146
151
AspA21-N-H…O(2)-EGCG
GlnA23-(Cα)-N-H…O(6)-EGCG
GlyA16C=O…H(12)O- EGCG
HypA18C=O…H(9)O- EGCG
HypA18C=O…H(3)O- EGCG
AlaA20-N-H…O(2)- EGCG
3.3
3.26
2.99
2.82
2.9
3.13
147
146
140
162
156
143
Total and contact surface areas of the collagen like triple helix and polyphenols in Å2
Collagen(24mer)
Cat
EGCG
PGG
Gal
CSA
1164
120
163
275
84
TSA
3825
268
382
688
160
CSA – Contact surface area
TSA – Total Surface Area
Solvent inaccessible surface areas of the complexes in Å2
Gal
Cat
EGCG
PGG
AT
BT
AT
BT
AT
BT
AT
BT
Ser
92
61
110
78
219
124
462
205
Hyp
85
65
120
75
248
115
421
197
Lys
151
82
176
94
279
135
357
189
Asp
102
71
112
76
186
115
514
238
Asn
84
69
124
86
214
125
368
196
AT – Solvent inaccessible Total Surface Area
BT – Solvent inaccessible Contact Surface Area
TSA of the complexes are in the range of 3840 – 4160
CSA of the complexes are in the range of 1160 – 1250
Plot of interfacial interacting volume Vs Binding energy of the
complex
Interacting Interfacial Volume (Å3)
Plot of effective solvent inaccessible contact volume Vs Binding
energy of the complex (inset): Plot of effective solvent inaccessible
contact surface area Vs Binding energy of the complex
Plot of inverse of interacting interfacial volume
(1/Int.Vol.) Vs inverse of binding energy(1/B.E) of the
complexes
 Ligation phenomena in collagen is being influenced by
geometric parameters
 Collagen complexation with small polyphenolic molecules,
there may exist some minimum geometrical sizes and binding
energies for influencing the long range ordering processes
 Ability of polyphenol bearing flavanoid structure in
management of arthritis and tanning may well result from
their ability to reduce accessibility of solvent(water) to
molecular surfaces of collagen
 The present investigation offers the possibility to understand
further recognition of phenomena associated with proteinprotein and DNA-protein interactions in general, based on
interfacial volume and surface areas