Harris et al.
Lester F. Harris*, Michael R. Sullivan, Pamela D. Popken-Harris
and David F. Hickok
Abbott Northwestern Hospital Cancer Research Laboratory
800 E. 28th St., Minneapolis, MN 55407
Correspondence should be addressed to: Lester F. Harris, PhD.
Keywords: DNA protein complexes, molecular dynamics simulations, site-specific recognition,
estrogen receptor, vitellogenin.
We investigated protein/DNA interactions, using molecular dynamics simulations
computed between a 10 Angstrom water layer model of the estrogen receptor (ER)
DNA binding domain (DBD) amino acids and DNA of an estrogen response
element (ERE) consisting of 25 nucleotide base pairs. This ERE nucleotide sequence
occurs naturally upstream of the Xenopus laevis vitellogenin A1 gene.
Hydrogen bonding interactions were monitored. In addition, van der Waals and electrostatic
interaction energies were calculated. Amino acids of the ER DBD DNA recognition
helix formed both direct and water mediated hydrogen bonds at cognate codon-
anticodon nucleotide base and backbone sites within the ERE DNA right major
groove half-site. These interactions together induced breakage of Watson-Crick
nucleotide base pairing hydrogen bonds, resulting in significant structural changes
and bending of the DNA into the protein.
The steroid hormone receptor proteins are made up of a family of sequence related
DNA regulatory proteins which share common structural modules within their
DNA binding domains (DBDs) (1). The DBDs consist of two zinc binding motifs
encoded by separate exons (2,3). Adjacent to the first zinc binding motif is a DNA
recognition alpha helix (4). Amino acids of this recognition helix specifically
interact with nucleotide base sites within the DNA major groove half-sites of the proteins' cognate DNA
binding sites. The DNA sites to which the steroid hormone receptor proteins specifically bind are referred
to as hormone response elements (HREs) (5). There are differences in nucleotide
sequence among the HREs to which the proteins specifically bind (6). Likewise,
there are differences in amino acid sequence within the DNA recognition helices of the steroid receptor
proteins (4). These differences suggest the existence of a site specific DNA
Our laboratory has long been interested in DNA site specific recognition by DNA
regulatory proteins and has made several key observations. Earlier, we reported
that genetic information is conserved between c-DNA sub-sequences which encode
DNA regulatory proteins' DNA binding domains (DBDs) and their cognate sites on
DNA to which they specifically bind (4,7,8). As an example, using genetic
sequence search techniques, we were the first to locate and describe the
Glucocorticoid Receptor (GR) DNA recognition alpha helix on the carboxyl
terminus of the first zinc binding motif. We discovered the GR DNA recognition
helix by observing that its encoding c-DNA sequence shares genetic information
with a glucocorticoid response element (GRE) (4). We compared the genetic
sequences of other members of the steroid hormone receptor family to the
glucocorticoid receptor sequence. Using this technique, we located putative DNA
recognition helices, adjacent to the first zinc binding motif, within the DBDs for
other members of the steroid receptor family . This conservation of genetic
information prompted us to hypothesize a code for DNA site specific recognition
for DNA regulatory proteins. We proposed that DNA site specific recognition is
based on stereochemical complementarity between amino acids of the proteins'
DBDs and their codon-anticodon nucleotides within cognate DNA binding sites.
Recently, we reported atomic interactions from molecular dynamics simulations in
solvent between amino acids of the GR DBD in complex with nucleotides within the
DNA major groove half-sites of its GRE and flanking regions (9,10). We observed
that amino acids of the GR DBD DNA recognition helix interacted with their
cognate codon-anticodon nucleotides within the GRE. These findings strongly
support our hypothesis for a site specific DNA recognition code as described above.
In the present study, we report that genetic information is conserved between the
Estrogen Receptor (ER) DBD
(GenBank locus HSERR) and
EREs located upstream of the Xenopus laevis vitellogenin A1 gene
(GenBank locus XLVITA15).
By model building, we observed that amino acids within the ER DBD
DNA recognition helix and adjacent beta strand are aligned with their cognate
codon-anticodon nucleotides within the ERE DNA major groove half-sites. These
findings suggested that amino acids of the ER DBD may interact with their cognate
codon-anticodon nucleotides within the ERE DNA major groove half-sites. To
investigate this possibility, we conducted 300 picoseconds of molecular dynamics
simulations on a model of the ER DBD/ERE complex in a 10 Angstrom water layer.
Hydrogen bonding interactions were monitored. In addition, van der Waals and
electrostatic interaction energies were calculated. The findings indicate that ER
DBD amino acids of the DNA recognition helix and beta strand form both direct
and water mediated hydrogen bonds at their cognate codon-anticodon nucleotide
base and backbone sites within the ERE DNA major groove half-sites. These
interactions together induce breakage of Watson-Crick nucleotide base pairing
hydrogen bonds, resulting in significant structural changes and bending of the DNA
toward the protein.
MATERIALS AND METHODS
The model of the ER DBD dimer used in this study was based on atomic
coordinates derived from X-ray crystallography of the ER DBD (11)
(PDB structure ID:
A model of B-form DNA of a naturally occurring ERE from
(GenBank locus XLVITA15)
in which we observed genetic similarity with the ER DBD (12) was
likewise created using the NUCLEIC ACID BUILDER module from the QUANTA program
(13). Solvated molecular dynamics simulation of the ER DBD/ERE
model is described below.
The solvated molecular dynamics simulations were run on a CRAY YMP C-90
supercomputer using a specially optimized version of CHARMm (release version
22.1) which has an atom limit of 15,000. The 10 Angstrom water layer model
required 6717 water atoms, the ER/ERE protein/DNA complex consisted of 2908
atoms resulting in a model of 9625 total atoms. The molecular dynamics simulation
required 0.6 CRAY C-90 CPU hours of computational resources per picosecond of
The solvated model was minimized for 200 cycles using the Steepest Descents
method. Then the structure was minimized for 100 cycles using the Adopted Basis
Newton-Rapson method. Heating was run for 600 cycles, at 0.001 ps per cycle for
a total of 0.6 picoseconds, resulting in 0.5 K temperature increase per cycle (from 0
to 300 degrees K). Equilibration was run for 1000 cycles (1 picosecond) resulting
in an overall temperature RMS deviation of approximately 5 degrees K. Finally molecular dynamics
were run with a step size of 0.001 picoseconds for an additional 300 picoseconds using velocity scaling.
A constant dielectric potential with an E value of 1.00 was used. A non-bonded cutoff of 15.00 angstroms
was used. Non-bonded parameters were updated every 20 cycles and all energy terms were computed (see
figure 1). For a detailed discussion of the CHARMm potential energy function
see reference (14) and for a review of molecular dynamics implementation in the
biological sciences see reference
Explicit sodium counter-ions were used in the DNA model, based on geometry
provided by Don Gregory Ph.D. from Molecular Simulations Inc. Zinc atoms were
placed in the ER structure and tetrahedrally coordinated with the sulfur atoms
from the "zinc-finger" cysteines. The residue topology file (RTF) for the "zinc-
finger" cysteines was altered and a new residue type was created 'ZCY' (for zinc
binding cysteine) in which the negative charges on the sulfur atoms were
increased from -0.19 to -0.50 so that the charges from the four tetrahedrally
coordinated cysteine sulfur atoms would neutralize the +2.0 charge on the zinc
atom. In addition, the charges on the zinc binding cysteine beta carbons were
increased from +0.19 to +0.40 and the charges on the alpha carbons were increased
from +0.10 to +0.20 in order to maintain the ZCY residue at a net 0.0 charge.
DNA Groove Geometry Calculations
The conformational changes of the DNA during dynamics were evaluated using the
CURVES 4.1program provided by Richard Lavery of Laboratoire de Biochimie Theorique
CNRS (personal communication). The documentation provided describes CURVES as "an
algorithm for calculating a helical parameter description for any irregular nucleic
acid segment with respect to an optimal, global helical axis. The solution is
obtained by minimizing a function which represents the variations in helical
parameters between successive nucleotides as well as quantifying the kinks and
dislocations which exist between successive helical axis segments". For more
detailed information regarding the CURVES 4.1 program see references
Interaction Energy Calculations
Interaction energies were calculated using CHARMm (14,15) between ERE
nucleotides and selected ER DBD amino acids from the right monomer of the 10
Angstrom water layer ER DBD/25 base pair ERE model after energy minimization,
heating and equilibration (0 picoseconds) and after 300 picoseconds of molecular
dynamics . Interaction energy was calculated using a constant dielectric potential
with an E value of 1.00. "Total Energy" is the sum of electrostatic interaction
energy and Van der Waals interaction energy. The values given for the interaction
of particular amino acid and nucleotide residues are the sum of the interaction
energies of all atoms in those residues.
Hydrogen Bond Calculations
The hydrogen bond interactions for the 10 Angstrom water layer ER/ERE model were recorded at 1.0
picosecond (1000 cycle) intervals. We used a distance-angle algorithm to compute hydrogen bonds which
was based on the results of analysis of hydrogen bonding in proteins (18). The
value used for the
maximum distance allowed between the hydrogen atom and the acceptor was 2.5 angstroms. The value
used for the maximum distance allowed between the atom bearing the hydrogen and the acceptor was 3.3
angstroms. The minimum angle at the acceptor was 90 degrees (limit = 0 to 180 degrees). The minimum
angle at the hydrogen was 90 degrees (limit = 0 to 180 degrees). The minimum angle at the atom bearing
the hydrogen was 90 degrees (limit = 0 to 180 degrees).
RESULTS AND DISCUSSION
Conservation of Genetic Information
We reported elsewhere that nucleotide sub-sequence similarity exists between well
characterized EREs and flanking nucleotides upstream of the Xenopus laevis
Vitellogenin A1 gene start site and the c-DNA which encodes amino acids of the ER
DBD (12 ). The nucleotide sequence we compared to the
ER DBD c-DNA contains two EREs; however, only the ERE site proximal to the Xenopus laevis
Vitellogenin A1 gene transcription start site has the "consensus" ERE recognition motif, TGACC, in both
DNA major groove half-sites. The distal "non-consensus" ERE
contains the sequence TGACT in both major groove half-sites. We observed that
primary nucleotide sub-sequence similarity between the ERE and flanking nucleotide
sites occurred only with the c-DNA sequence of exon 2 which encodes the first zinc
binding motif and DNA recognition helix of the ER DBD (see figure 2a and
We also observed that the c-DNA which encodes the ER DNA recognition helix
shares sub-sequence similarity only with the proximal "consensus" ERE site (see
figure 2b). However, by examining coding possibilities in all three reading
on both strands of the "non-consensus ERE", we observed codon sites, embedded in
overlapping reading frames, for amino acids of the exon 2 encoded ER DNA
recognition helix and exon 3 encoded beta strand (see figure 2c). Furthermore,
model building we observed that amino acids encoded at the splice junctions of
exons 2 and 3 of the ER DBD are aligned with their cognate codon-anticodon
nucleotides within the "non-consensus" ERE right and left major groove half-sites.
This includes amino acids of the ER DNA recognition helix encoded in exon 2 and
a beta strand encoded in exon 3 at the splice junction of exons 2/3
(see figure 3a-f).
The above findings suggested that the amino acids within the ER DBD DNA
recognition structures may interact with their cognate codon-anticodon nucleotides
within the "non-consensus" ERE and its flanks. To investigate this possibility, we
docked the ER DBD dimer at H-bonding distance within the DNA major groove
half-sites of the ERE. Using the CHARMm program, we conducted 300 picoseconds
of molecular dynamics. An ER DBD/ 25 base pair ERE model, without the water
molecules, is shown in figure 4. In this model the ER DBD is docked at
approximately 10 Angstroms from the 25 base pair ERE and flanking nucleotides for
visual clarity. This model is to be used as a key for locating interactions found
between the ER DBD amino acids and nucleotides of the ERE and its flanks during
molecular dynamics, see table I.
Amino Acid-Nucleotide Hydrogen Bonding Interactions
Hydrogen bonding interactions between amino acids encoded by exons 2 and 3 of
the ER DBD and nucleotides of the ERE were monitored. A summary of H-
bonding interactions is shown in table I. Equivalent functional sites on the
acids are grouped: Lysine hydrogen bond donor sites HZ1, HZ2 and HZ3 are
combined as HZ. Arginine hydrogen bond donor sites HH11 and HH12 are
combined as HH1 and hydrogen bond donor sites HH21 and HH22 are combined as
HH2. Glutamine hydrogen bond donor sites HE21 and HE22 are combined as HE2.
Glutamic acid hydrogen bond acceptor sites OE1 and OE2 are combined as OE.
Likewise, the DNA backbone phosphate group hydrogen bond acceptor sites O1P
and O2P are combined as OP. First and last occurrences of DNA/protein hydrogen
bonds which includes minimization, heating and equilibration steps followed by the
300 picosecond production dynamics simulation are given in picoseconds of
dynamics with their frequency of occurrence. Frequencies of H-bonding interactions
(shown in table I) greater than 300 reflect multiple hydrogen bonds (i.e. when two
or more of the grouped atoms from one residue interact at the same atom from
another residue) for a given amino acid/nucleotide interaction. The hydrogen
bonding interactions between amino acids encoded by exons 2 and 3 of the ER DBD
and nucleotides of the ERE were monitored. Individual hydrogen bonds are labeled
"C" for amino acid-nucleotide codon interactions, "AC" for amino acid-nucleotide
anticodon interactions, "C*" and "AC*" for amino acid-nucleotide codon and
anticodon interactions when the codon or anticodon sequence is present reading 3'
to 5'. It can be seen in table I that the majority of H-bonding interactions for exon 2
encoded amino acids E203, K206, and K210 of the ER DNA recognition helix
occur at codon-anticodon nucleotide sites within the ERE right major groove
half-site. Likewise, H-bonding interactions between the ERE right major groove
half-site and the exon 3 encoded amino acids K235, S236, and Q238 occur at codon-
anticodon nucleotide sites. In contrast, in the left ERE DNA major groove half-site,
none of the amino acids of the DNA recognition helix encoded in exon 2 form H-
bonds at codon-anticodon sites. However, amino acids K235 and S236 encoded in
exon 3 form H-bonds at codon-anticodon nucleotide sites, see table I.
Electrostatic and van der Waals interactions
We calculated van der Waals and electrostatic interaction energies between amino
acids of the ER DBD and nucleotides on the sense and antisense strands of the ERE.
Calculations were performed on the minimized, heated and equilibrated structures
at the beginning of the dynamics simulation and after 300 picoseconds in order to
analyze the attractive forces between ER DBD DNA recognition helix amino acids
and ERE nucleotides. A total energy (Kcal/M) interaction consisting of both van
der Waals and electrostatic energy was determined. Total energy values were
recorded for the hydrophilic amino acids of the ER DNA recognition helix and
nucleotide base pairs within the ERE DNA right major groove half-site. Glutamic
acid 203 has been reported to be important in DNA site specific recognition by the
ER protein (11). As can be seen in table I, during the 300 picosecond molecular
dynamics Glu 203 forms a direct specific H-bond with the H61 base site of its central codon nucleotide
A32, reading 3'- to - 5,' 5'-AAG-3'. However, the energy
potential for Glu 203 and nucleotide A32 after 300 picoseconds has an overall
positive, repulsive, value, (see figure 5a left). A close-up of Glu 203
A32 is shown in figure 5a right. A hydrogen bond occurs between
Glu 203 sidechain site OE2 and A32 nucleotide base site H61; as expected, a negative,
attractive, value is seen between OE2 and H61 sites. An extensive network of water
mediated H-bonds also occur between Glu 203 and sites on nucleotides A31, A32
and G33, (see table I and figure 6a). These water
mediated interactions together
dampen the overall repulsive energy of the base sites of nucleotide A32 and serve to
position the Glu 203 sidechain site OE 2 within direct H-bonding distance of the
H61 base site of nucleotide A32. Total interactive energy values were also recorded
between ERE nucleotides and ER DBD amino acids Lys 206, Lys 210, Gln 214, Lys
235 and Gln 238 sidechains. In all cases, attractive energy values were observed
between these amino acids and their cognate codon or anticodon nucleotide base
pairs found within the ERE DNA right major groove half-site (see figure 5b-f).
addition, specific H-bonds were formed between the sidechains of Lys 206, Lys 210,
Lys 235 and Gln 238 and their cognate codon-anticodon nucleotide sites
(see table I and figure 6b,c,e and f).
Specific Amino Acid-Nucleotide Interactions
Genetic information is conserved within the ERE right major groove half-site for
amino acids of the exon 2 encoded ER DNA recognition helix Amino acids (see
figure 2c and figure 3). In addition, we also observed that genetic information is
conserved within both the ERE left and right major groove half-sites for amino acids
of the zinc binding motif encoded within exon 3. Amino acids Lys 206, Lys 210
and Arg 211 of the ER DNA recognition helix are conserved at similar positions
within the DNA recognition helices of members of the steroid receptor family
(4); these amino acids of the ER DNA recognition helix have been reported to
specifically bind DNA at ERE sites (11). We observed that amino acids Lys 206,
and Lys 210 form both direct and water mediated multidentate H-bonds at cognate codon-anticodon
nucleotide base sites within the ERE right major groove half-site, as shown in table
I see figure 2c and figure 3a-h for reference. Close up views of specific
amino acid-nucleotide H-bonding interactions are shown in figure 6a-f. In figure 6a,
a direct H-bond occurs between amino acid Glu 203 and its codon nucleotide A32
(reading 3'-to-5'). Water mediated H-bonds between the sidechain of Glu 203 and
its codon nucleotides A31 and G33 (reading 3'-to-5') are also shown. In figure 6b,
direct and water mediated H-bonding between Lys 206 and codon nucleotides A32
and G33 respectively are shown. In figure 6c, direct and water mediated H-
bonding interactions for amino acid Lys 210 and codon nucleotide G33 are shown.
In figure 6d, direct H-bonds are formed between Arg 211 and non- codon
nucleotide G16. A water mediated H-bond between Arg 211 and non-codon
nucleotide T34 is also shown. In figure 6e, direct H-bonds between exon 3
Lys 235 and its codon nucleotide G39 are shown. Direct and water mediated H-
bonds between exon 3 encoded amino acid Gln 238 and its anticodon nucleotides
T15 and T14 respectively are shown in figure 6f.
Nucleotide-Nucleotide Hydrogen Bonding Interactions for the 25 bp ERE DNA
Hydrogen bonding interactions between sense and antisense strand ERE nucleotides
during 300 picoseconds of molecular dynamics on the ER DBD/ERE 25 bp DNA
model are shown in table II. A loss of one or more canonical Watson -Crick
H-bonds can be seen occurring predominantly in the right major groove half-site.
This is especially evident at nucleotide base pairs: G16-C35, A17-T34, and C18-
G33. The majority of the loss in canonical H-bonds for these nucleotide base pairs
can be accounted for by amino acid-nucleotide interactions at WC sites as shown in
table I and by the non-canonical nucleotide-nucleotide H-bonding
shown in table II. In the left major groove half-site a loss of canonical WC H-
occurs between the nucleotide base pair C6-G45 at their H42-06 and N3-H1 base
sites. Nucleotide base pair T9-A42 also shows loss of WC H-bonding at the H3-N1
Structural Changes in ER DBD Protein/ERE DNA Complex
During molecular dynamics of the ER DBD/ERE complex, structural changes occur
in the DNA (see figure 7a-e). The DNA appears to wrap around the ER DBD
recognition alpha helices. The minor groove between the left and right ERE major
groove half-sites is compressed. The nucleotides in particular within the ERE right
major groove half-site show a loss of canonical WC base pairing H-bonds
(see table II). A close-up view of the ERE right major groove nucleotide sequence is shown in
figure 7d. A loss of WC canonical H-bonding is apparent at nucleotide pairs
C35, A17-T34 and C18-G33, see figure 7e. To further illustrate the geometric
changes in the ERE DNA, using the CURVES program (16,17), ERE DNA
major and minor groove width was analyzed after 300 picoseconds of molecular
dynamics for the ER DBD/ERE model compared to ERE DNA at 0 picoseconds
(see figure 8). The DNA major and minor groove widths determined at 0
picoseconds, 11.4 and 5.6 Angstroms, respectively are in close agreement with
values reported for canonical B-DNA duplexes (17). These values were used to
monitor changes in DNA major and minor groove width during molecular
dynamics. An increase in width in the ERE right major groove half-site can be seen.
A decrease in minor groove width between the ERE DNA major groove half-sites
was also observed. These changes in DNA structure reflect loss of nucleotide base
pair WC H-bonding which facilitate bending of the DNA into the ER DBD protein.
Similar findings of DNA bending have been reported for the ER/ERE and other
DNA regulatory protein/DNA complexes (19-21).
These conformational changes can be viewed as interactive molecules
(see figure 9) and as MPEG movies
(see figure 10).
Our findings, reported herein, show that amino acids Lys 206, Lys 210, and Gln
214 of the ER DNA recognition helix encoded in exon 2 and Lys 235 and Gln 238
of the exon 3 encoded ER DBD second zinc binding motif have electrostatic
attraction for their codon-anticodon nucleotides within the ERE right major groove
half-site, see figure 5. In addition, these amino acids, with the exception of
specifically form both direct and water mediated H-bonds at their cognate codon-
anticodon nucleotide base and backbone sites, (see table I and figure 6).
Furthermore, Glu 203 forms direct and water mediated H-bonds with its codon
nucleotides A31, A32 and G33, reading 3'-to-5', 3'-GAA-5' (see table I and
figure 6a). Although an arginine codon-anticodon nucleotide site is not found within the
ERE DNA major groove half-sites, the nucleotide trimer TGA does occur. This
sequence closely resembles the arginine codon CGA having a T substituted for C
thus conserving the pyrimidine at position one of the CGA arginine codon. In
addition, the T substitution conserves the stereochemical complementarity between
nucleotide base acceptor sites of TGA, as seen with CGA, and the arginine
sidechain functional donor sites. Hydrogen bonding interactions between arginine
residues of the ER DBD and nucleotides of the ERE occur within the TGA
sequence with direct H-bonding interactions occurring predominately at nucleotide
base sites on G of the TGA sequence (see table I
and figure 6d). Therefore
codon-anticodon nucleotides within the ERE DNA right major groove half-site by
amino acids of the ER DNA recognition helix and the exon 3 encoded ER DBD
second zinc binding motif offer an explanation for the ER DNA binding preference
to ERE major groove half-sites.
Recently, a protein/DNA structure of an ER DBD/ERE complex consisting of an
imperfectly palindromic ERE was determined by X-ray crystallography at 2.6A
resolution (22). In this study, the right half-site of the ERE contained the "consensus"
sequence, 5'-TGACCT-3'- 5'-AGGTCA-3', and the left half-site
contained a "non-consensus " sequence, 5'-AAGTCA-3'- 5'-TGACTT-3'.
Hydrogen bonding interactions were reported between nucleotides of the "non-
consensus" ERE half-site and amino acids of the ER DBD (22). The right half-
site of the ERE nucleotide sequence used in our study reported herein is identical to the 5'-AAGTCA-3'-
5'-TGACTT-3' "non-consensus" ERE sequence above
(22). Furthermore, the H-bonding interactions reported herein between ER DBD
amino acids Tyr 195, His 196, Tyr 197, Glu 203, Gly 204, Lys 210, Lys 211, Arg 211, Arg 234, Lys 235,
Gln 238, and Arg 241 and nucleotides of the "non-consensus" ERE sequence (see table I, right column ) are in agreement with the findings reported for the same sequence
in the X-ray crystallography structural determination of the
ERE/ER DBD complex (22).
Our observations indicate that ER site specific DNA recognition involves
overlapping reading frames. In addition, our findings also suggest that site specific
DNA recognition may be bi-directional, that is, amino acids may recognize their
cognate codon-anticodon nucleotides reading 5'-to-3' or 3'-to-5'. This appears to be
the case for Glu 203 of the ER DNA recognition helix as described above. These
observations offer an explanation as to why more than one amino acid can interact
with the same nucleotide and vise-versa and still satisfy site specific DNA
recognition according to our hypothesis. Our findings reported herein and
elsewhere indicate that conservation of genetic information
(4,7-10,12) is correlated
with both DNA site specific recognition and transcription enhancement.
Our findings strongly support the idea of a stereo-chemical basis for the origin of
the genetic code (23-32) because amino acids within regulatory proteins' DNA
recognition helices are consistently being found lining up with cognate codon-anticodon nucleotides
within their specific DNA binding sites (4,7-10,12). These findings also suggest
that these structures may have been template dependent in their evolution (i.e. peptides acting as
templates for nucleotide polymerization or vice-versa (33-35). The findings of
conservation of genetic information between the exon splice junction sites of the ER DBD and its cognate
ERE are identical to the findings we reported elsewhere for the glucocorticoid receptor protein and its
cognate glucocorticoid response elements (8). Therefore, we propose that prebiotic,
template directed autocatalytic synthesis of mutually cognate peptides and
polynucleotides resulted in their amplification and evolutionary conservation in
contemporary eukaryotic organisms as a modular genetic regulatory apparatus.
Finally, the amino acid-nucleotide atomic interactions described herein and
elsewhere confirm our original prediction that conservation of genetic information
is a determinate of site specific DNA recognition for DNA regulatory proteins
We thank Don Gregory of Molecular Simulations Inc. for providing geometry for explicit sodium counter-
ions used in all simulations and for Zn atom placement and charge parameters for Zn binding cysteines in
the "zinc fingers" of the ER DBD structures. We also thank the Molecular Simulations Inc. staff for
software support with QUANTA, Michael Fenton of Fentonnet Inc. for data reduction programs, Barry
Bolding of Minnesota
Supercomputer Center for CHARMm software optimization on the CRAY C-90, Minnesota
Supercomputer Institute Scientific Director, Don Truhlar for support and encouragement, the Minnesota
Supercomputer Center user services representatives for technical support on the CRAY C-90,
R. Lavery for providing CURVES 4.1
software and special thanks are due to Charlie Larson of Silicon Graphics Inc. for hardware support with
the IRIS 4D 320-GTX workstation. This work was supported in part by a research grant from the
Minnesota Supercomputer Institute, Minneapolis MN. This work was also supported by a research
fellowship dedicated to the memory of William Lang Jr..
It is indeed with sadness that we report that our colleague
Dr. David F. Hickok
passed away on June 5,
1996. This manuscript is dedicated to his memory.
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