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WSN: Protein Science (vol.4, #4)
(from URL: gopher://orion.oac.uci.edu/protein/)
AU - Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS
TI - Principles of protein folding--A perspective from
simple exact models
AD - Ken A. Dill, Department of Pharmaceutical Chemistry,
Box 1204, University of California, San Francisco,
California 94143-1204; e-mail: dill@maxwell.ucsf.edu.
AB - General principles of protein structure, stability, and
folding kinetics have recently been explored in
computer simulations of simple exact lattice models.
These models represent protein chains at a rudimentary
level, but they involve few parameters, approximations,
or implicit biases, and they allow complete
explorations of conformational and sequence spaces.
Such simulations have resulted in testable predictions
that are sometimes unanticipated: The folding code is
mainly binary and delocalized throughout the amino acid
sequence. The secondary and tertiary structures of a
protein are specified mainly by the sequence of polar
and nonpolar monomers. More specific interactions may
refine the structure, rather than dominate the folding
code. Simple exact models can account for the
properties that characterize protein folding: two-state
cooperativity, secondary and tertiary structures, and
multistage folding kinetics--fast hydrophobic collapse
followed by slower annealing. These studies suggest the
possibility of creating ``foldable'' chain molecules
other than proteins. The encoding of a unique compact
chain conformation may not require amino acids; it may
require only the ability to synthesize specific monomer
sequences in which at least one monomer type is
solvent-averse.
SO - Protein Science 1995;4:561-601
AU - Bodkin MJ, Goodfellow JM
TI - Competing interactions contributing to alpha-helical
stability in aqueous solution
AD - Julia M. Goodfellow, Department of Crystallography,
Birkbeck College, Malet Street, London WC1E 7HX, UK; e-
mail: ubcg08a@uk.ac.bbk.ccs.
AB - The stability of a 15-residue peptide has been
investigated using CD spectroscopy and molecular
simulation techniques. The sequence of the peptide was
designed to include key features that are known to
stabilize alpha-helices, including ion pairs, helix
dipole capping, peptide bond capping, and aromatic
interactions. The degree of helicity has been
determined experimentally by CD in three solvents
(aqueous buffer, methanol, and trifluoroethanol) and at
two temperatures. Simulations of the peptide in the
aqueous system have been performed over 500 ps at the
same two temperatures using a fully explicit solvent
model. Consistent with the CD data, the degree of
helicity is decreased at the higher temperature. Our
analysis of the simulation results has focused on
competition between different side-chain/side-chain and
side-chain/main-chain interactions, which can, in
principle, stabilize the helix. The unfolding in
aqueous solution occurs at the amino terminus because
the side-chain interactions are insufficient to
stabilize both the helix dipole and the peptide
hydrogen bonds. Loss of capping of the peptide backbone
leads to water insertion within the first peptide
hydrogen bond and hence unfolding. In contrast, the
carboxy terminus of the alpha-helix is stable in both
simulations because the C-terminal lysine residue
stabilizes the helix dipole, but at the expense of an
ion pair.
SO - Protein Science 1995;4:603-612
AU - Bagley SC, Altman RB
TI - Characterizing the microenvironment surrounding protein
sites
AD - Russ B. Altman, Section on Medical Informatics,
Stanford University School of Medicine, MSOB X-215,
Stanford, California 94305-5479; e-mail:
altman@camis.stanford.edu.
AB - Sites are microenvironments within a biomolecular
structure, distinguished by their structural or
functional role. A site can be defined by a three-
dimensional location and a local neighborhood around
this location in which the structure or function
exists. We have developed a computer system to
facilitate structural analysis (both qualitative and
quantitative) of biomolecular sites. Our system
automatically examines the spatial distributions of
biophysical and biochemical properties, and reports
those regions within a site where the distribution of
these properties differs significantly from control
nonsites. The properties range from simple atom-based
characteristics such as charge to polypeptide-based
characteristics such as type of secondary structure.
Our analysis of sites uses nonsites as controls,
providing a baseline for the quantitative assessment of
the significance of the features that are uncovered. In
this paper, we use radial distributions of properties
to study three well-known sites (the binding sites for
calcium, the milieu of disulfide bridges, and the
serine protease active site). We demonstrate that the
system automatically finds many of the previously
described features of these sites and augments these
features with some new details. In some cases, we
cannot confirm the statistical significance of
previously reported features. Our results demonstrate
that analysis of protein structure is sensitive to
assumptions about background distributions, and that
these distributions should be considered explicitly
during structural analyses.
SO - Protein Science 1995;4:622-635
AU - Hodel A, Rice LM, Simonson T, Fox RO, Brunger AT
TI - Proline cis-trans isomerization in staphylococcal
nuclease: Multi-substate free energy perturbation
calculations
AD - Axel T. Brunger, Department of Molecular Biophysics and
Biochemistry, Bass Center, Room 434, Yale University,
266 Whitney Avenue, New Haven, Connecticut 06520; e-
mail: brunger@laplace.csb.yale.edu.
AB - Staphylococcal nuclease A exists in two folded forms
that differ in the isomerization state of the Lys 116-
Pro 117 peptide bond. The dominant form (90% occupancy)
adopts a cis peptide bond, which is observed in the
crystal structure. NMR studies show that the relatively
small difference in free energy between the cis and
trans forms ([Delta]G_cis to trans[nearly equal] 1.2
kcal/mol) results from large and nearly compensating
differences in enthalpy and entropy ([Delta]H_cis to
trans[nearly equal][Delta]TS_cis to trans[nearly equal]
10 kcal/mol). There is evidence from X-ray crystal
structures that the structural differences between the
cis and the trans forms of nuclease are confined to the
conformation of residues 112-117, a solvated protein
loop. Here, we obtain a thermodynamic and structural
description of the conformational equilibrium of this
protein loop through an exhaustive conformational
search that identified several substates followed by
free energy simulations between the substates. By
partitioning the search space into conformational
substates, we overcame the multiple minima problem in
this particular case and obtained precise and
reproducible free energy values. The protein and water
environment was implicitly modeled by appropriately
chosen nonbonded terms between the explicitly treated
loop and the rest of the protein. These simulations
correctly predicted a small free energy difference
between the cis and trans forms composed of larger,
compensating differences in enthalpy and entropy. The
structural predictions of these simulations were
qualitatively consistent with known X-ray structures of
nuclease variants and yield a model of the unknown
minor trans conformation.
SO - Protein Science 1995;4:636-654
AU - Morita EH, Shirakawa M, Hayashi F, Imagawa M, Kyogoku Y
TI - Structure of the Oct-3 POU-homeodomain in solution, as
determined by triple resonance heteronuclear
multidimensional NMR spectroscopy
AD - Yoshimasa Kyogoku, Institute for Protein Research, Osaka
University, 3-2 Yamadao-ka, Suita, Osaka 565, Japan.
AB - The POU-homeodomain (POU_H) forms the bipartite DNA-
binding POU domain in association with the POU-specific
domain. The 1H, 15N, and 13C magnetic resonances of the
67-amino acid long POU_H of mouse Oct-3 have almost
completely been assigned, mainly through the combined
use of three-dimensional triple resonance NMR methods.
Based on the distance and dihedral angle constraints
derived from the NMR data, the solution structure of
the POU_H domain has been calculated by the ab initio
simulated annealing method. The average RMS deviation
for all backbone heavy atoms of the 20 best calculated
structures for residues 9-53 of the total 67 amino acid
residues is 0.44 Angstrom. The POU_H domain consists of
three alpha-helices (helix-I, 10-20; helix-II, 28-38;
and helix-III, 42-53), and helices-II and -III form a
helix-turn-helix motif. In comparison with other
classical homeodomains, the folding of the three
helices is quite similar. However, the length of helix-
III is fairly short. In the complex of the Oct-1 POU
domain with an octamer site (Klemm JD, et al., 1994,
Cell 77:21-32), the corresponding region is involved in
helix-III. The structural difference between these two
cases will be discussed.
SO - Protein Science 1995;4:729-739
AU - Zhang Y -Z, Paterson Y, Roder H
TI - Rapid amide proton exchange rates in peptides and
proteins measured by solvent quenching and two-
dimensional NMR
AB - In an effort to develop a more versatile quenched
hydrogen exchange method for studies of peptide
conformation and protein-ligand interactions, the
mechanism of amide proton exchange for model peptides
in DMSO-D_2O mixtures was investigated by NMR methods.
As in water, H-D exchange rates in the presence of 90%
or 95% DMSO exhibit characteristic acid- and base-
catalyzed processes and negligible water catalysis.
However, the base-catalyzed rate is suppressed by as
much as four orders of magnitude in 95% DMSO. As a
result, the pH at which the exchange rate goes through
a minimum is shifted up by about two pH units and the
minimum exchange rate is [approximately equal to]100-
fold reduced relative to that in D_2O. The solvent-
dependent decrease in base-catalyzed exchange rates can
be attributed primarily to a large increase in pK_a
values for the NH group, whereas solvent effects on
pK_W seem less important. Addition of toluene and
cyclohexane resulted in improved proton NMR chemical
shift dispersion. The dramatic reduction in exchange
rates observed in the solvent mixture at optimal pH
makes it possible to apply 2D NMR for NH exchange
measurements on peptides under conditions where rates
are too rapid for direct NMR analysis. To test this
solvent-quenching method, melittin was exchanged in D_2
O (pH 3.2, 12 degrees C), aliquots were quenched by
rapid freezing, lyophilized, and dissolved in quenching
buffer (70% DMSO, 25% toluene, 4% D_2O, 1% cyclohexane,
75 mM dichloroacetic acid) for NMR analysis. Exchange
rates for 21 amide protons were measured by recording 2
D NMR spectra on a series of samples quenched at
different times. The results are consistent with a
monomeric unfolded conformation of melittin at acidic
pH. The ability to trap labile protons by solvent
quenching makes it possible to extend amide protection
studies to peptide ligands or labile protons on the
surface of a protein involved in macromolecular
interactions.
SO - Protein Science 1995;4:804-814
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