High-Resolution Protein Design with
Backbone Freedom
Pehr B. Harbury,*Joseph J. Plecs, Bruce Tidor, Tom
Alber, Peter S. Kim
Recent advances in computational techniques have allowed the design
of precise side-chain packing in proteins
with predetermined, naturally
occurring backbone structures. Because these methods do not
model protein main-chain flexibility,
they lack the breadth to explore novel backbone conformations.
Here the de novodesign
of a family of-helical bundle proteins
with a right-handed superhelical
twist is
described. In the design,
the overall protein fold was specified by hydrophobic-polar
residue patterning, whereas the bundle oligomerization state,
detailed main-chain conformation,
and interior side-chain rotamers
were engineered by computational enumerations of packing in
alternate backbone structures. Main-chain flexibility was incorporated
through an algebraic parameterization of the backbone. The
designed
peptides form -helical
dimers,trimers, and tetramers in accord with the design
goals. The crystal structure of the tetramer matches the designed
structure in atomic detail.
P. B. Harbury is at the Whitehead Institute
for Biomedical Research, Howard Hughes Medical Institute and Department
of Biology, Massachusetts Institute of Technology, Nine Cambridge Center,
Cambridge, MA 02142, USA, and Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School,
Boston, MA 02115, USA. J. J. Plecs is in the Department
of Molecular and Cell Biology and Department
of Physics, University of California at Berkeley, Berkeley, CA 94720, USA.
B. Tidor is in the Department of Chemistry,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA. T. Alber
is in the Department of Molecular and
Cell Biology, University of California at Berkeley, Berkeley, CA 94720,
USA. P. S. Kim is at the Whitehead Institute for Biomedical Research, Howard
Hughes Medical Institute and Department
of Biology, Massachusetts Institute of Technology, Nine Cambridge Center,
Cambridge, MA 02142, USA.
* Present address: Department
of Biochemistry, Stanford University, Stanford, CA 94305, USA.
To whom correspondence
should be addressed. E-mail:
dvorak@wi.mit.edu
Proteins exhibit precise geometric packing of atoms
in their interiors. Nevertheless, empirical protein
design
methods have achieved a measure of generality and simplicity
by ignoring detailed interactions
between amino acid residues. These
design
approaches rely instead on imitation of statistical sequence
patterns in naturally occurring proteins, such as hydrophobic-polar
residue patterns, amino acid secondary structure propensities,
and characteristic local interaction motifs (1).
Perhaps as a direct consequence, many designed
proteins exhibit fluctuating or "molten" interiors (2),
and some assume unintended tertiary
conformations (3).
Packing in proteins has been studied computationally by holding the
protein main chain in the wild-type conformation (the "fixed-backbone"
approximation) and asking which sets of amino acid side
chains can efficiently fill the interior space (4).This
technique has been used successfully to repack wild-typeside
chains into predetermined backbone
structures (5) and has more recently been
extended to the design
of amino acid sequences. Fixed-backbone design
based on naturally occurring backbone templates has produced
proteins that fold to the target structures with high thermal
stabilities (6).
However, fixed-backbone methods are unable to model
protein main-chain flexibility. Thus, main-chain adjustments known tooccur
in response to core mutations in proteins (7)are not
allowed. Moreover, the fixed-backbone approach has a severelimitation when
applied to backbone structures for which a naturallyoccurring example does
not exist. Although naturally occurringbackbone coordinates represent the
ground-state conformation forat least one sequence (the naturally occurring
sequence), thisassumption is not necessarily valid for arbitrary backbone
coordinates.When the backbone structure is
designed
de
novo, a complete set of
plausible backbone conformations must be sampled to identify
structures that lie at a free-energy minimum in the sequence and
conformational spaces.
These limitations may be overcome by treating the backbone as a parametric
family of structures rather than as a static entity (8).
A small but well-defined subset of
main-chain conformations can then be exhaustively sampled in
a finite time. For example, coupled searches of side-chain
packing and main-chain conformation under
a parametric coiled-coil backbone model
have been used to reproduce detailed,
crystallographically observed conformations for coiled-coil
proteins (8).
A true test of the utility of parametric-backbone models
in protein
design would be to engineer
a protein fold for which no structural example is known. We
report here the computational design
of a family of dimeric, trimeric, and tetrameric -helicalbundles
with a right-handed superhelical structure.
Although a nuclear magnetic resonance (NMR) structure of a right-handed
dimer of helices in
detergent
micelles has been reported (9), no structures
of trimeric or tetrameric right-handed
coiled coilsexist. The x-ray crystal structure of the tetrameric bundle
designedhere matches the predicted
structure in atomic detail, adopting
an unprecedented, but
deliberately
engineered, right-handed superhelical
fold.
Design principles. The first step
of our design is based on an analysis
of the hydrophobic-polar residue pattern in left-handed
coiled coils. The superhelical twist of left-handedcoiled
coils arises from a small difference between the integralfrequency of the
heptad repeat and the characteristic frequencyof
helices (10). Each amino acid in a straight helix
rotates about 100 degree radially around the helix axis (360 degree
for 3.6 residues). Seven amino acids rotate 700 degree lagging
two full turns (720 degree by 20 degree A sevenfold repeat,
therefore, forms a left-handedstripe
in a straight helix (Fig.
1). In a left-handedsupercoiled
conformation that evolves 20 degree every seven residues,this stripe can
always face toward the axis of superhelical rotation(Fig.
1).
Fig. 1. (Left) Sevenfold hydrophobic repeats give rise
to left-handed coiled coils, and 11-fold
repeats to right-handed coiled coils.
(A) A heptad repeat in a regular
helix produces a left-handed stripe
and a left-handed supercoil. This arrangement
is schematically illustrated alongside
the standard sevenfold helical wheel projection for coiled coils. (B)
An undecatad repeat in a regular
helix produces a right-handed stripe
and a right-handed supercoil. The 11-fold
helical wheel projection is illustrated. H, hydrophobic residue; P, polar
residue; +/, charged residue.
Fig. 2. (Right) Calculating the effects of sequence changes
on unfolding free energies, illustrated for an isoleucine-to-valine substitution
at position a of a right-handed coiled-coil
dimer. The top panels show axial projections of one right-handed
and one left-handed coiled coil. The
top left panel differs from the top right panel by interchange of the amino
acid at position a of the right-handed
coiled coil with the amino acid at position f of the left-handed
coiled coil. The lower panels show the unfolded
polypeptides. Each leg of the thermodynamic
cycle is labeled with a letter. The legs labeled A and B correspond to
unfolding of the wild-type and mutant coiled-coil sequences respectively.
The legs labeled C and D correspond to residue permutation in the folded
and unfolded states, respectively.
Because the cycle is closed, the difference in the two unfolding free energies
is equal to the difference in the two permutation free energies: A
B = C D. The A and
B legs are a sum of two terms, the unfolding free energy for the right-handed
coiled coil,GRHunfold,
and the unfolding free energy for the left-handed
coiled coil,GLHunfold.
Expanding A and B and rearranging terms gives [GRHunfold,
(I at a) - GRHunfold,
(V at a)] = C D + [GLHunfold
(I at f) - GLHunfold,
(V at f)]. For the computational studies reported here (, ), D was assumed
to be 0 kcal/mol, C was computed from the bonded,
van der Waals and hydrogen bonding
terms of the CHARMM19 potential () and a solvent accessible surface hydration
potential (), and [GLHunfold,
(V at f) - GLHunfold,
(I at f)] was taken from experimentally measured free energies of unfolding
(). Differences in calculated stability are dominated by the CHARMM19 potential,
which accounts for 80% of the variance in the calculated stabilities of
right-handed coiled-coil sequences.
The surface hydration potential and left-handed
coiled-coil unfolding free energies each account for ~10% of the variance
in the calculated stabilities. [View
Larger Versions of these Images (27 + 49K GIF file)]
Application of this principle to an 11-fold (undecatad)
amino acid repeat suggests that a right-handed
supercoil should form. Eleven amino acids rotate about 1100
degree which leads three full turns (1080 degree by 20 degree
Thus, an undecatad repeat produces
a right-handed stripe in
a straight helix, which should
give rise to a right-handedsupercoil
(Fig. 1). Examination of an 11-residue helical-wheel
projection indicates that amino acids in the first, fourth, and
eighth positions (positions a, d, and h) fall on the same surface
of the helix. These considerations
suggest that a 3-4-4 hydrophobic repeat might specify a right-handed
coiled coil.
The second step of our design consisted
of determining which amino acids can
pack the core of a right-handed bundle
with a 3-4-4 hydrophobic repeat, and by their shapes direct
dimer, trimer, or tetramer formation. Detailed
dimer, trimer, and tetramer right-handedcoiled
coils were modeled for all possible
core sequences madeup of the small
aliphatic amino acids alanine, valine, norvaline,leucine, isoleucine, and
alloisoleucine. Alloisoleucine, the stereoisomerof isoleucine with inverted
chirality at the C carbon, was
included in the design
calculation because preliminary models
suggested the need for a residue that would orient side-chain
volume into a trans1
dihedral angle in its most commonly occurring rotamer. Norvaline
(an n-propyl side chain) was
used as a general straight-chain analog for methionine and lysine
(11). These six amino acids could be placed
at the core positions a, d, and h in 216 (63) possible
sequences. However, because most of the amino acids have multiple
side-chain conformations, about 25
possible side-chain rotamers
exist at each position. For simplicity, the design
calculations were limited to the 11 lowest energy rotamers at
each core position in each oligomeric state, as determined
by single-level packing calculations (12).
Thus, 3993 (3 x 113) structures (ignoring variations in backbone
conformation) were generated for the design
analysis.
Computation. To model the
right-handed structures, we modified
a technique previously used to predict crystal structures of
natural left-handed coiled coils (8,
12).
For each of the 3993 core rotamer conformations, main-chain coordinates
were determined by exploring
a parametric family of superhelix backbones described
originally by Francis Crick (13). The parametric
backbone algebra for left-handed coiled
coils was altered to reflect an 11-fold amino acid repeat. Periodic
boundary conditions were applied, and two-, three-, or fourfold
rotational symmetry was imposed around the superhelix axis.
For the computational studies, alanine residues were placed
at the exterior positions of the undecatad
repeat (positions b, c, f, g, and j), and -aminobutyric
acid residues (an ethyl side chain)
were placed at positions on the boundary of the hydrophobic
core (positions e, i, and k). As the backbone coordinate search
for each core rotamer conformation required ~3 min on a MIPS
R3000 processor, the entire calculation took about 8 days.
A difficult aspect of protein design
is the need to compare unfolding free energies for different candidate
amino acid sequences. The effects of sequence changes on unfolding
free energies can be calculated as the difference in the free
energy of mutation in the folded
and unfolded states (14).
To avoid explicitly modeling
the unfolded state, which consists
of a large ensemble of conformations, we modified this basic
strategy by calculating an energy of permutation: the energy
difference between two different covalent arrangements of the
same amino acids (Fig. 2). Whereas energies
of mutation are seldom zero, an energy of permutation will be
zero if the amino acid side chains
do not interact with each other, which we assume to be the case
in the unfolded state. Importantly,
conformation-independent
energetic biases for one amino acid over another in the underlying
potential energy function are canceled in a permutation difference.
The permutation used here interchanges an amino acid at position
f of a left-handed coiled
coil with an amino acid in the hydrophobic core of a right-handedcoiled
coil. Using experimentally measured unfolding free energiesof f-substituted
left-handed coiled coils (15),
and assuming that the free energy of permutation in the unfolded
state is zero, we derived
calculated unfolding energy differences for different undecatad
sequences in the right-handed model
conformation (16).
Experimentally observed structures. Two criteria were used to
choose optimal core sequences for each oligomeric state. First,
the stability of the sequence in the target conformation was
required to be high. Second, the specificity of the sequence for
forming the target conformation, instead of the two alternative oligomeric
states, was maximized. We took the following approach: (i) Within
each oligomeric state, the mean stability averaged over the
entire family of 216 possible sequences was tabulated; stabilities
of individual sequences were expressed as standard deviations
from this mean. (ii) Because equilibria between different oligomerization
states depend on monomer concentration
and on residues outside
of the hydrophobic core, we calculated specificities using an
arbitrary standard state that factors out these considerations.For
each equilibrium, the free energy of interconversion was assigneda value
of zero when averaged over all 216 core sequences. Specificitieswere thus
evaluated by taking the stability difference (in kilocaloriesper mole)
for each sequence between the target conformation andthe alternative oligomeric
conformations, and expressing the differencesin units of standard
deviation.
Dimer, trimer, and tetramer core sequences thus identified
(Table 1) were inserted into a common 33-residue templateto
generate the peptides RH2, RH3, and
RH4 (Fig. 3). The template contains positively
charged lysine residues on one side
of the hydrophobic core and negatively charged glutamate residues
on the other side to favor parallel
helix arrangements over antiparallel arrangements (17).
Two norvaline residues at positions h of the dimer sequence
pack against glutamate residues at positions k in the neighboring
helix and were therefore substituted with the isosteric amino
acid lysine. Charged and polar residues were placed at the exterior
positions of the template to ensure high solubility, and a single
tyrosine residue was includedto facilitate
concentration
determination. The RH
peptides were prepared by
solid-phase synthesis and purified by reversed-phase high-performance
liquid chromatography (18).
Table 1. Top sequence solutions for right-handed
dimer, trimer, and tetramer coiled coils according to the packing calculation.
The table consists of three lists, the first sorted according to dimer
stability, the second according to trimer stability, and the third according
to tetramer stability.
|
Sequence
|
Stability |
Specificity§ |
a |
d |
h |
|
Dimer |
|
Dimer-trimer |
Dimer-tetramer |
|
nV |
L |
nV |
2.0 |
0.9 |
1.3 |
nV |
nV |
L |
1.9 |
0.8 |
0.7 |
nV |
L |
L |
1.9 |
0.7 |
0.9 |
I |
L |
nV* |
1.8 |
1.8 |
1.0 |
Trimer |
|
Trimer-dimer |
Trimer-tetramer |
|
nV |
aI |
L |
2.6 |
0.3 |
0.5 |
I |
aI |
L |
2.4 |
0.5 |
0.2 |
I |
aI |
nV |
2.4 |
0.6 |
0.6 |
nV |
aI |
nV |
2.3 |
0.6 |
0.4 |
L |
aI |
L |
2.0 |
0.1 |
0.8 |
aI |
aI |
I* |
2.0 |
1.9 |
2.0 |
Tetramer |
|
Tetramer-dimer |
Tetramer-trimer |
|
nV |
aI |
I |
3.1 |
2.2 |
1.7 |
nV |
aI |
L |
2.6 |
0.6 |
0.5 |
L |
aI |
I* |
2.5 |
1.9 |
2.0 |
L |
aI |
L |
2.3 |
0.3 |
0.8 |
|
* The core sequences chosen
for RH2, RH3, and RH4 are indicated by asterisks. These sequences were
chosen on the basis of two criteria: high predicted stabilities in the
target conformation, and high predicted preference for the target conformation
over the two competing alternatives. Thus, large positive values in both
the stability and the specificity columns were required. |
Residues present at positions a, d, and h for each sequence in the table
(28). |
Within each oligomerization state, the stabilities of individual sequences
are expressed in units of standard
deviation
from the mean stability of all 216 possible sequences (see text). More
positive values indicate larger predicted stability. |
§ Specificity of
each sequence for the target conformation over the two competing conformations
(for example, the list sorted on dimer stability shows the dimer-over-trimer
and dimer-over-tetramer specificities). More positive values indicate larger
predicted specificities for the target conformation (see text). |
|
Fig. 3. Helical wheel projection of residues Ala1
to Ala33 of the RH coiled-coil template sequence (28).
View is from the NH2-terminus, and residues in the first three
helical turns are boxed or circled. Undecatad
positions are labeled a through k. The full template sequence consists
of three undecatads. The peptides
RH2, RH3, and RH4 differ only by the amino acids present at positions a,
d, and h (18). The sequences (with positions a, d,
and h in italics; aI, alloisoleucine; and nV, norvaline) are the following.
RH2-AE IEQ LKKEnVAYL IKK LKAEKLAE
IKK
LKQEKA
RH3-AEaIEQaIKKE IAYLaIKKaIKAEILAEaIKKaIKQEIA
RH4-AE LEQaIKKE IAYL LKKaIKAEILAE
LKKaIKQEIA
The template sequence was chosen to contain positively charged lysine
residues at position e on one side
of the helix and negatively charged glutamate residues at positions g and
k on the opposite side to favor a parallel
association of helices in a helical bundle. [View
Larger Version of this Image (22K GIF file)]
On the basis of circular dichroism (CD) measurements at 10 mM
peptide concentration in neutral pH
phosphate-buffered saline (PBS) at 4 degree C, RH2 appears to
be ~80% helical, whereas RH3 and RH4 appear to be >95% helical
(19) (Fig. 4A). Under
these conditions, RH2 displays a broad thermal unfolding transition,
RH3 exhibits a cooperative melt with an apparent melting temperature
(Tm) of 95 , and RH4 has a thermal stability thatexceeds
100°C (Fig. 4B). In the presence of the denaturant
guanidinium hydrochloride (GdmCl)
at 3 M concentration, RH4 melts cooperatively with an apparent
Tm of 90 . Thus, whereas RH2 appears to be
incompletely folded under
physiologic conditions, RH3 andRH4 form well-structured and extremely stable
helical structures.
Fig. 4. The RH2 (open circles), RH3 (open triangles), and RH4
(open squares) peptides form two-,
three-, and four-stranded helical bundles.
(A) CD spectra at 4 degree C in PBS (pH 7.0) and 10 mM
peptide concentration (19).
The mean residue ellipticity, [], is
reported in units of 103 degrees
cm2 dmol-1. (B) Thermal melts monitored by
CD at 222 nm (19). The filled squares show data for
RH4 collected in the presence of 3 M GdmCl, a denaturant.
(C) Analytical ultracentrifugation data (32 krpm) collected at 4
degree C in PBS (pH 7.0) at ~100 µM peptide
concentration (22). The natural logarithm of the absorbance
at 235 nm is plotted against the square of the radial position. Dashed
lines with increasing slopes indicate, respectively, the predicted data
for dimer, trimer, and tetramer bundles. (D) Aromatic and amide-proton
NMR spectra of the RH4 peptide at different
times after transfer into D2O (21). The
inset shows the volume of one amide
resonance (the peak labeled with an arrow) plotted against exchange time.
The data closely fit a single exponential decay
with a half-life of ~10 days. [View
Larger Version of this Image (37K GIF file)]
Sedimentation equilibrium measurements (20) were
used to
determine the oligomerization
state of each peptide undernative
conditions (Fig. 4C). As intended
in the design, the RH2 peptide
sediments approximately as a dimer, the RH3 peptidesediments
approximately as a trimer, and the RH4 peptide
sediments approximately as a tetramer. The RH3 and RH4 peptides
exhibit no systematic
dependence
of molecular weight on concentration between 20 µM and
200 µM. The molecular weight of the RH2 peptidesystematically
decreases at concentrations below 100
µM (presumably because of dissociation in the low micromolar
concentration range) but exhibits no systematic
deviation
from dimer molecular weight between 200 µM and 2 mM. Thus,
each of the RH peptides assumesthe
oligomerization state for which it was designed.
To assess whether the designed oligomers
associate in a "molten" fashion or with fixed tertiary structures, we studied
the dynamic properties of RH3 and RH4 by hydrogen-deuterium
amide-proton exchange (21)
(Fig. 4D). Relative to poly D,L-alanine,
the most slowly exchanging protons in RH3 were protected by
a factor of >105, whereas the most slowly exchanging protons
in RH4 were protected by a factor of >107. These
protection factors are comparable to protection factors observed
for the native states of naturally occurring proteins. The trimer
and tetramer structures thus appear to assemble with native-like
rigidity.
To evaluate the high-resolution features of the design,
we determined the x-ray crystal structure
of the RH4 peptide at 1.9 A
resolution (22). The RH4 structure was refined toa
conventional
R-factor of 20.4% with a free R-factor of 24.8%
and root mean square deviations
from ideal bond lengths and bondangles
of 0.009 A and 1.97 degree respectively. The designed
peptide forms the intended
parallel, right-handed superhelix structure(Fig.
5A). Moreover, the side-chain packing
observed in the RH4 crystal structure closely matches that predicted
by the design calculation
(Fig. 5B). The engineered and observed rotamers
for the core side chains are identical.
The crystal structure differs from the designed
conformation primarily at the COOH-terminus where crystal contacts
cause the superhelix to be locally underwound.
Such end effects were deliberately
ignored by the design method
in the interest of simplicity (8). Core side-chain
and main-chain atom positions in the central undecatadof
the crystal structure differ from atom positions in the calculatedmodel
by a root mean square
deviation of
0.20 ÅThe superhelical parameters (8,
13)
(radius R0, frequency0,
and phase angle ) for the
designed
structure and the NH2-terminaltwo undecatads
of the crystal structure are as follows: R0 = 7.29 A 0
= 1.5 centiradians per residue, and
= 11 A for the model, and
R0
= 7.49 A 0 = 1.6 centiradians
per residue, and = 10 degree for the
crystal structure. Thus, the experimentally observed structure for
the RH4 peptide matches the designed
structure in atomic
detail.
Fig. 5. Crystal structure of RH4. (A) Axial view of the
left-handed GCN4-pLI tetramer (27)
next to the right-handed RH4 tetramer
(22). The view is from the NH2-terminus
looking toward the COOH-terminus. Purple van der
Waals surfaces identify residues at
the a positions, green surfaces identify
residues at the d positions, and yellow surfaces identify
residues at the h positions. (B) Superposition of the central undecatad
of the calculated (red) and crystallographically observed (blue) structures
of RH4. Three cross-sections of the superhelix, centered at positions a,
d, and h, are shown. In each case the calculated side-chain
packing conformation matches the conformation observed in the crystal structure
(11). (C) Superposition of the calculated (red)
and crystallographically observed (blue) backbone conformations of the
right-handed tetramer. [View
Larger Versions of these Images (47 + 41K GIF file)]
Practical implications. Our results demonstrate
that empirical protein design principles
combined with computational protein engineering methods can
be used to predict and designnovel
backbone structures, with root mean square coordinate errorsthat approach
0.2 A. This level of precision is encouraging withregard to the feasibility
of designing protein catalysts, which
may require the accurate positioning of reactive groups. Methods
to engineer buried electrostatic interactions and to calculate
accurately their energetic effects (23) should
providea second high-resolution design
tool that is effectively orthogonal to engineered van der
Waals packing. Efforts to parameterize the backbones of more
complex protein folds have begun (24), and
it will be interesting to see the extent to which the parametric-backboneapproach
to protein design presented here can
be generalized.
REFERENCES AND NOTES
-
W. F. Degrado,
Adv.
Protein Chem. 39, 51 (1988)[ISI][Medline];
M. H. Cordes, A. R. Davidson, R. T.
Sauer, Curr. Opin. Struct. Biol. 6, 3 (1996)[ISI][Medline];
R. Aurora, T. P. Creamer, R. Srinivasan, G. D. Rose, J. Biol. Chem.272,
1413 (1997)[ISI][Full
Text]; C. E. Schafmeister, S. L. LaPorte, L. J. Miercke,
R. M. Stroud, Nature Struct. Biol. 4, 1039 (1997)[ISI][Medline].
-
W. F. DeGrado,
D. P. Raleigh, T. Handel, Curr.
Opin. Struct. Biol. 1, 984 (1991);
S. F. Betz, D. P. Raleigh, W. F. DeGrado,
ibid.3,
601 (1993); J. W. Bryson,
et al.,
Science 270, 935 (1995)[ISI][Abstract].
-
C. P. Hill, D. H. Anderson,
L. Wesson, W. F. DeGrado, D. Eisenberg,
Science
249, 543 (1990)[ISI][Medline];
B. Lovejoy, et al., ibid.259, 1288 (1993)[Medline].
-
K. E. Drexler, Proc. Natl.
Acad. Sci. U.S.A. 78, 5275 (1981)[ISI];
C. Pabo, Nature 301, 200 (1983)[ISI][Medline];
J. W. Ponder and F. M. Richards, J.
Mol. Biol. 193, 775 (1987)[ISI][Medline].
-
P. E. Correa, Proteins7,
366 (1990)[ISI][Medline];
C. Lee and S. Subbiah, J. Mol. Biol. 217, 373 (1991)[ISI][Medline];
L. Holm and C. Sander, ibid.218,
183 (1991)[Medline];
P. Tuffery, C. Etchebest, S. Hazout, R. Lavery, J. Biomol. Struct. Dyn.8,
1267 (1991)[ISI][Medline];
J. Desmet, M. D. Maeyer, B. Hazes,
I. Lasters, Nature 356, 539 (1992)[ISI];
P. Koehl and M. Delarue, J. Mol.
Biol. 239, 249 (1994)[Medline];
C. Lee, ibid.236, 918 (1994)[Medline].
-
J. R. Desjarlais
and T. M. Handel, Protein Sci.4,
2006 (1995)[ISI][Medline];
G. A. Lazar, J. R. Desjarlais, T. M.
Handel, ibid.6, 1167
(1997)[Medline];
B. I. Dahiyat and S. L. Mayo, Science 278, 82 (1997)[ISI][Abstract/Full
Text]; B. I. Dahiyat, C. A. Sarisky, S. L. Mayo, J.
Mol. Biol. 273, 789 (1997)[ISI][Medline];
S. M. Malakauskas and S. L. Mayo, Nature Struct. Biol. 5,
470 (1998)[Medline];
J. W. Bryson, J. R. Desjarlais, T.
M. Handel, W. F. DeGrado,
Protein
Sci. 7, 1404 (1998)[ISI][Medline];
H. W. Hellinga, Nature Struct. Biol. 5, 525 (1998)[ISI][Medline].
-
T. Alber, et al., Science239,
631 (1988)[ISI][Medline];
E. P. Baldwin, O. Hajiseyedjavadi, W. A. Baase, B. W. Matthews, ibid.262,
1715 (1993)[Medline].
-
P. B. Harbury, B. Tidor, P.
S. Kim, Proc. Natl. Acad. Sci. U.S.A. 92, 8408 (1995)[ISI][Abstract].
-
The transmembrane helices
of the erythrocyte protein glycophorin A have been shown to form a right-handed
dimer in detergent micelles [ K. R.
MacKenzie, J. H. Prestegard, D. M. Engelman, Science 276,
131 (1997)[ISI][Abstract/Full
Text]]. There are hints that other right-handed
superhelical assemblies exist in nature. Repeating 11-fold motifs proposed
to form right-handed coiled coils have
been found in several naturally occurring proteins, including D-7 Lea proteins
from cotton seeds and the tetrabrachion membrane surface protein of Staphylothermus
marinus [ L. Dure, Plant J. 3, 363 (1993)[ISI][Medline];
J. Peters, H. Baumeister, A. Lupas, J. Mol. Biol. 257, 1031
(1996)[ISI][Medline]].
Helices M4 and M6 of SERCA1a, the Ca2+ adenosine
triphosphatase of fast-twitch skeletal muscle sarcoplasmic reticulum, have
been proposed on the basis of disulfide
cross-linking data to form a right-handed
coiled coil that lines the Ca2+ channel [ W. J. Rice, N. M.
Green, D. H. MacLennan, J. Biol. Chem. 272, 31412 (1997)[ISI][Abstract/Full
Text]]. Our right-handed
superhelical structures may provide
useful models for studying this family
of proteins.
-
F. H. C. Crick, Acta Crystallogr.6,
689 (1953).
-
For the nonnatural amino
acids norvaline and alloisoleucine, six possible rotamers (- and t for 1;
-, +, and t for 2) were tested. Notation:
-, -60°; +, +60°; t, 180°.
-
Design
calculations were performed on coiled-coil models
containing alanine at positions b, c, f, g, and j; -amino
butyric acid at positions e, i, and k; and all possible combinations of
the residues alanine, valine, leucine, isoleucine, alloisoleucine and norvaline
at positions a, d, and h. Optimal conformations were identified
as described in (8) with the following
modifications. First, the helix
frequency in Crick's parameterization (1)
was set to 6/11 radians per amino acid to ensure
a regular undecatad repeat. Second,
the superhelix frequency (w0) of the initial backbone coordinates
was set to 2 centiradians per amino acid and then explored in both the
positive and negative directions until the potential minimum with respect
to superhelix frequency had been located. Third, single-site enumerations
(for example, with alanine at positions a and d and a variable residue
at position h) were performed initially to identify
good symmetrical single-level packing rotamers. The values of the a-position
orientation angles () were required to lie
between 3° and 32°
for these calculations (for an undecatad
repeat, one full asymmetric unit in
covers 360/11 = 32.7°; larger changes in
produce symmetry-related structures that differ only in the assignment
of the undecatad repeat). The 11 single-level
packings with the largest calculated stabilities at each position (a, d,
and h) were then combined in all possible combinations to construct undecatad
packings. Each of the six amino acids under
consideration was represented at least
once at each core position.
-
F. H. C. Crick, Acta Crystallogr.6,
685 (1953).
-
B. L. Tembe and J. A. McCammon,
Comput.
Chem. 8, 281 (1984)[ISI];
D. L. Beveridge and F. M. DiCapua, Annu. Rev. Biophys. Biophys. Chem.18,
431 (1989)[ISI][Medline].
-
K. T. O'Neil and W. F. DeGrado,
Science
250, 646 (1990)[Medline].
-
Unfolding free energy differences
(G) between sequences were calculated
with the thermodynamic cycle illustrated in
Fig. 2. An
advantage of using a thermodynamic pathway is that it avoids double counting
of contributions to stability. The G's
of permutation in the folded state,
corresponding to step C, were approximated in three steps. First, transfer
free energies of the native coiled coils from water to vacuum were estimated
from the accessible hydrophobic surface areas of their lowest energy conformations
[ B. Lee and F. M. Richards, J. Mol. Biol. 55, 379 (1971)[ISI][Medline]],
assuming an average transfer free energy of 0.012 kcal/(mol·A2)
(25). Second, free energies of permutation in vacuo were approximated as
CHARMM19 (26) potential differences between the lowest energy packings
of the native coiled coils and the lowest energy packings of the permuted
coiled coils. All bonded potentials,
the Lennard-Jones potential (switched off between 6.0 and 6.5 Å),
and the explicit hydrogen-bond potential in the polar EF2 configuration
[ L. Nilsson and M. Karplus, J. Comput. Chem. 7, 591 (1986)[ISI]]
were used. Finally, transfer free energies of the permuted coiled-coil
sequences from vacuum to water were estimated from the accessible hydrophobic
surface areas of their lowest energy conformations. Our approximation of
relative stability derives from the
assumptions that (i) translational, rotational, and electronic contributions
to the classical partition function roughly cancel in the difference, (ii)
the lowest potential energy-packing conformations dominate the partition
sums, and (iii) the entropic contributions from the vibrational properties
of the lowest potential energy-packing conformations roughly cancel in
the difference.
-
O. D. Monera, C. M. Kay,
R. S. Hodges, Biochemistry 33, 3862 (1994)[ISI][Medline].
-
Peptides
were synthesized and purified as described
[ D. J. Lockhart and P. S. Kim, Science 257, 947 (1992)[Medline]].
The identities of the peptides
were confirmed by mass spectrometry (Perceptive Biosystems Voyager Elite),
and all molecular masses were found to be within 1 dalton of the expected
mass. The peptides have acetylated
NH2-termini and amidated COOH-termini.
-
CD spectra were measured
on an Aviv 60DS spectropolarimeter. Measurements of []222
were made at 4°C in 50 mM phosphate
(pH 7.0), 150 mM NaCl, and 10 µM peptide
concentration. A []222 value
of 35,000
degrees
cm2 dmol-1 was taken to correspond to 100% helix
[ P. Luo and R. L. Baldwin, Biochemistry36, 8413 (1997)[ISI][Medline]].
Thermal melts were performed in the same buffer and also, for RH4, with
the addition of 3 M GdmCl to facilitate unfolding. Values of
Tm
were estimated from []222
versus temperature data (in 2° steps) by evaluating the maximum of
d[]/dT-1
[C. R. Cantorand P. R. Shimmel, Biophysical Chemistry (Freeman,
New York, 1980), vol. 3, p. 1132]. Peptide
concentrations were determined spectrophotometrically
in 6 M GdmCl [ H. Edelhoch, Biochemistry6,
1948 (1967)[Medline]]
with an extinction coefficient of 1280 cm-1M-1 at
280 nm.
-
Analytical ultracentrifugation
measurements were carried out as described
in (27). All experiments were performed in 50 mM sodium phosphate (pH 7.0)
and 150 mM NaCl at 4°C. Data for RH3 and RH4 were collected at peptide
concentrations of 20, 70, and 200 µM, and showed no systematic dependence
of molecular weight on concentration. At concentrations below 100 µM,
the molecular weight of the RH2 peptide
varied systematically between monomer and dimer values. The data reported
here for RH2 were therefore collected at 200 µM, 700 µM, and
2 mM peptide concentrations and show
no systematic
dependence
of molecular weight on concentration. The molecular weights
derived
from the complete data sets (followed by expected molecular weight) and
[the rotor speeds in thousand revolutions per minute at which data were
collected] are as follows: RH2--8623 (7792) [30, 35]; RH3--13,087 (11,637)
[32]; RH4--15,833 (15,516) [27, 32].
-
One-dimensional 1H-NMR
spectra were recorded on a Bruker AMX
500 spectrometer as described [E. K.
O'Shea, K. J. Lumb and P. S. Kim, Curr. Biol. 3, 658 (1993)].
Measurements were made in D2O
containing 50 mM phosphate (pH 7.15), 150 mM NaCl (the pH is uncorrected
for the isotope effect), and 1 mM peptide.
Spectra were normalized on the volumes of a tyrosine aromatic proton resonance,
and peaks corresponding to the most slowly exchanging amide
protons were integrated and fit to a single exponential in time. Half-lives
of 161 min and 16,700 min were measured for the RH3 and RH4 peptides,
respectively. Following [ S. W. Englander,
N. W. Downer, H. Teitelbaum, Annu. Rev. Biochem. 41, 903
(1972)[ISI][Medline]],
poly D,L-alanine was calculated
to have a half-life of 8.3 × 10-4 min under
the conditions of the experiment. Thus the most slowly exchanging amide
protons in the RH3 and RH4 peptides
are protected by factors of 2 × 105 and 2 × 107,
respectively, relative to poly D,L-alanine.
Although these protection factors are quite large by comparison with protection
factors for most naturally occurring proteins, it is likely that they are
smaller than would be predicted by a global unfolding mechanism. It is
possible that for coiled coils in the extremely slow exchange regime, a
local exchange mechanism dominates [see S. W. Englander,
T. R. Sosnick, J. J. Englander, L.
Mayne, Curr. Opin. Struct. Biol. 6, 18 (1996)[ISI][Medline]
and references therein for a discussion of exchange mechanisms].
-
The RH4 peptide
was crystallized by vapor diffusion from 100 mM tris (pH 8.1), 0.3 M NaBr,
20% isopropanol, and 20% polyethylene glycol 1450. The crystals had P4212
symmetry (unit cell dimensions: a = b= 37.56 Å, c
=
53.38 Å) with one monomer in the asymmetric unit. Data to 1.9 Å
resolution were collected at room temperature with an R-Axis image plate
detector
(3175 unique reflections,
Rmerge = 3.4%; Rmerge
= I
- I/I,
where I is the intensity of a reflection). The predicted structure,
which included core side
chains at positions a, d, and h, -amino
butyric acid at positions e, i, and k, and alanine elsewhere, was used
in a combined rotation-translation search (with 6 to 2.9 Å data)
along the crystallographic fourfold axis with the program X-PLOR [ A. T.
Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)].
The coordinates corresponding to the peak solution (initial R =
49.6%) were annealed and rebuilt into simulated-annealing omit maps with
the program O [ T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta
Crystallogr. A47, 110 (1991)[ISI]].
When the model reached an R-factor
of ~22.0% (R factor = Fobs
- Fcalc)/Fobs,
where
Fobs and Fcalc are the observed
and calculated structure factors, respectively), annealing no longer resulted
in improvement. Alternating cycles of manual rebuilding and Powell minimization
led to a final R-factor of 20.4% and a free
R-factor (calculated
for 10% of the data not used for refinement) of 24.8% [ A. T. Brünger,
Nature
355, 472 (1992)].
The final model, which includes
33 residues of peptide sequence (Glu2,
Glu4, Lys15, and Glu24 do not have clear
side-chain
density
and are modeled as alanine), 8 water
molecules, and 3 isopropanol molecules, exhibits root mean square deviations
from ideal bond lengths and bond angles
of 0.009 Å and 1.97°, respectively. All main-chain torsional
angles fall within the helical region of a Ramachandran plot. The coordinates
have been deposited in the Brookhaven
Protein Data Bank (accession code #1RH4).
-
B. Honig and A. Nicholls,
Science
268, 1144 (1995)[ISI][Medline].
-
A. G. Murzin, A. M. Lesk,
C. Chothia, J. Mol. Biol. 236, 1369 (1994)[ISI][Medline].
-
P. L. Privalov and G. I.
Makhatadze, J. Mol. Biol. 232, 660 (1993)[ISI][Medline].
-
B. R. Brooks et al., J.
Comput. Chem.
4, 187 (1983).
-
P. B. Harbury, T. Zhang,
P. S. Kim, T. Alber, Science 262, 1401 (1993)[ISI][Medline].
-
Abbreviations for the amino
acid residues are A, Ala; E, Glu; I, Ile; K, Lys; L, Leu; Q, Gln; Y, Tyr;
nV, nor-Val; aI, allo-Ile.
-
We gratefully acknowledge
M. Burgess for peptide synthesis, C.
Lockshin, L. Stern, and A. Rich for use of their rotating anode
and image-plate detector, J. Harris
for assistance with the preparation of figures, A. Keating and R. Varadarajan
for comments on the manuscript, and Z. Y. Peng, D. J. Lockhart, and members
of the Kim laboratory for insightful discussions and criticism throughout
the course of this work. This research was supported by NIH grants (GM55758
to B.T., GM48598 to T.A., and GM44162 to P.S.K.).
14 August 1998; accepted 14 October 1998
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Volume 282, Number 5393 Issue of 20 Nov 1998, pp. 1462 - 1467
©1998 by The American Association for the Advancement of Science.