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1.
For predicting solvent accessibility from the sequence of amino acids in proteins, we use a logistic function trained on
a non-redundant protein database. Using a principal component analysis, we find that the prediction can be considered, in
a good approximation, as a monofactorial problem: a crossed effect of the burial propensity of amino acids and of their locations
at positions flanking the amino acid of interest. Complementary effects depend on the presence of certain amino acids (mostly
P, G and C) at given positions. We have refined the predictive model (1) by adding supplementary input data, (2) by using
a strategy of prediction correction and (3) by adapting the decision rules according to the amino acid type. We obtain a best
score of 77.6% correct prediction for a relative accessibility of 9%. However, compared to trivial strategy only based upon
the frequencies of buried or exposed residues, the gain is less than 4%.
Received: 4 June 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998 相似文献
2.
B. Tallur J. Nicolas A. Froger D. Thomas C. Delamarche 《Theoretical chemistry accounts》1999,101(1-3):77-81
We have worked with a classification method based upon a notion of probabilistic similarity or “likelihood of similarity”
between aligned sequences. One important parameter, among others, affecting the sequence similarities and hence the classification
results is the amino acid similarity matrix. We present a method for choosing the most adapted matrix to classify protein
sequences. This method has been applied to the transmembrane channels of the major intrinsic protein (MIP) family. At present,
two functional subgroups have been well characterized in this family: (1) specific water transport by the aquaporins and (2)
small neutral solutes transport. The aim of the present study is to show the usefulness of the classification method in the
prediction of sequence segments important for substrate selectivity. Moreover, we show that this method can also be used to
predict the function of undetermined MIP proteins. The method could be applied to other protein families as well.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
3.
Renato Colle Raffaele Montagnani Oriano Salvetti 《Theoretical chemistry accounts》1999,101(4):262-268
A molecular fragment approach is used to compute ionization potentials, transition energies and electron affinities of pyrrole
oligomers. The calculations of these quantities include correlation energy contributions evaluated by integrating a functional
of the two-particle Hartree-Fock density matrix. Pyrrole oligomers with chains of up to 16 rings are explicitly treated and
the calculated quantities extrapolated to the limit of an infinitely long chain, to predict polymer properties. The theoretical
results compare favorably with data on gas-phase ionization potentials deduced from experimental oxidation potentials, and
with optical absorption peaks recorded in solution or on solid films. The large discrepancy between electron affinities obtained
from the eigenvalues of an independent-particle frozen-orbital calculation and those obtained from separate, correlated calculations
on the neutral system and the negative ion in shown.
Received: 24 March 1998 / Accepted: 2 September 1998 / Published online: 7 December 1998 相似文献
4.
A. C. Camproux A. G. Brevern S. Hazout P. Tufféry 《Theoretical chemistry accounts》2001,106(1-2):28-35
The prediction of loop conformations is one of the challenging problems of homology modeling, owing to the large sequence
variability associated with these parts of protein structures. In the present study, we introduce a search procedure that
evolves in a structural alphabet space deduced from a hidden Markov model to simplify the structural information. It uses
a Bayesian criterion to predict, from the amino acid sequence of a loop region, its corresponding word in the structural alphabet
space. The results show that our approach ranks 30% of the target words with the best score, 50% within the five best scores.
Interestingly, our approach is also suited to accept or not the prediction performed. This allows the ranking of 57% of the
target words with the best score, 67% within the five best scores, accepting 16% of learned words and rejecting 93% of unknown
words.
Received: 17 July 2000 / Accepted: 5 January 2001 / Published online: 3 April 2001 相似文献
5.
Rajeev Prabhakar Margareta R. A. Blomberg Per E. M. Siegbahn 《Theoretical chemistry accounts》2000,104(6):461-470
A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and
glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid
side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their
backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric
cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather
fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement
with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems
except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways
form rings in which the separated charges can be stabilized.
Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000 相似文献
6.
A homotopy method is presented that locates both minimizers and saddle points of energy functions in an efficient manner.
In contrast to other methods, it makes possible the exploration of large parts of potential energy surfaces. Along a homotopy
path stationary points of odd and even order occur alternately. A path tracing procedure requiring only gradients and at most
one evaluation of the Hessian matrix is given. Test results on a model potential and three MINDO/3 potentials are reported.
Received: 6 May 1996 / Accepted: 2 April 1998 / Published online: 23 June 1998 相似文献
7.
The positions of a given fold always occupied by strong hydrophobic amino acids (V, I, L, F, M, Y, W), which we call “topohydrophobic
positions”, were detected and their properties demonstrated within 153 non-redundant families of homologous domains, through
3D structural alignments. Sets of divergent sequences possessing at least four to five members appear to be as informative
as larger sets, provided that their mean pairwise sequence identity is low. Amino acids in topohydrophobic positions exhibit
several interesting features: they are much more buried than their equivalents in non-topohydrophobic positions, their side
chains are far less dispersed; and they often constitute a lattice of close contacts in the inner core of globular domains.
In most cases, each regular secondary structure possesses one to three topohydrophobic positions, which cluster in the domain
core. Moreover, using sensitive alignment processes such as hydrophobic cluster analysis (HCA), it is possible to identify
topohydrophobic positions from only a small set of divergent sequences. Amino acids in topohydrophobic positions, which can
be identified directly from sequences, constitute key markers of protein folds, define long-range structural constraints,
which, together with secondary structure predictions, limit the number of possible conformations for a given fold.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998 相似文献
8.
A discrete-state ab initio protein structure prediction procedure is presented, based on the assumption that some proteins
fold in an hierarchical way, where the early folding of independent units precedes and helps complete structure formation.
It involves a first step predicting, by means of threading algorithms and local structure prediction methods, the location
of autonomous protein subunits presenting favorable local and tertiary interactions. The second step consists of predicting
the structure of these units by Monte Carlo simulated annealing using several database-derived potentials. In a last step,
these predicted structures are used as starting conformations of additional simulations, keeping these structures frozen and
including the complete protein sequence. This procedure is applied to two small DNA-binding proteins, 434 cro and the Drosophila melanogaster homeodomain that contain 65 and 47 residues, respectively, and is compared to the nonhierarchical procedure where the whole
protein is predicted in a single run. The best predicted structures were found to present root-mean-square deviations relative
to the native conformation of 2.7 ? in the case of the homeodomain and of 3.9 ? for 434 cro; these structures thus represent
low-resolution models of the native structures. Strikingly, not only the helices were correctly predicted but also intervening
turn motifs.
Received: 6 July 2000 / Accepted: 8 September 2000 / Published online: 21 December 2000 相似文献
9.
A large-scale one-centre expansion with a radial B-spline basis set is implemented for bound and continuum states. A Kohn-Sham
hamiltonian is employed with Hartree and exchange-correlation potentials calculated from the SCF electron density taken from
a previous LCAO calculation. An inverse iteration method is used to obtain the continuum wavefunction, from which the cross
section and asymmetry parameter are calculated. The convergence with respect to angular momentum and cut-off radius is analysed
for N2. The relevance of multipolar contributions even at large distances is shown and suggestions for further improvements are
given. In order to show that the present method is suitable to treat systems of moderate size, the (CH3)3N molecule has also been calculated and the results are compared with experiment.
Received: 19 May 1998 / Accepted: 20 August 1998 / Published online: 7 December 1998 相似文献
10.
Patricia Amara Martin J. Field Cristobal Alhambra Jiali Gao 《Theoretical chemistry accounts》2000,104(5):336-343
Hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials are becoming increasingly important for studying
condensed-phase systems but one of the outstanding problems in the field has been how to treat covalent bonds between atoms
of the QM and MM regions. Recently, we presented a generalized hybrid orbital (GHO) method that was designed to tackle this
problem for hybrid potentials using semiempirical QM methods [Gao et al. (1998) J Phys Chem A 102: 4714–4721]. We tested the method on some small molecules and showed that it performed well when compared to the purely
QM or MM potentials. In this article, we describe the formalism for the determination of the GHO energy derivatives and then
present the results of more tests aimed at validating the model. These tests, involving the calculation of the proton affinities
of some model compounds and a molecular dynamics simulation of a protein, indicate that the GHO method will prove useful for
the application of hybrid potentials to solution-phase macromolecular systems.
Received: 4 October 1999 / Accepted: 18 December 1999 / Published online: 5 June 2000 相似文献
11.
Adam Liwo Jarosław Pillardy Rajmund Kaźmierkiewicz Ryszard J. Wawak Małgorzata Groth Cezary Czaplewski Stanisaw Ołdziej Harold A. Scheraga 《Theoretical chemistry accounts》1999,101(1-3):16-20
A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups
as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization
methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original
rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures
of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding
simulations and more complicated motifs in inverse-folding simulations.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
12.
Martin Albrecht Peter Reinhardt Jean-Paul Malrieu 《Theoretical chemistry accounts》1998,100(1-4):241-252
A size-consistent ab initio formalism to calculate correlation corrections to ionization potentials as well as electron affinities
of periodic systems is presented. Our approach is based on a Hartree-Fock scheme which directly yields local orbitals without
any a posteriori localization step. The use of local orbitals implies non-zero off-diagonal matrix elements of the Fock operator,
which are treated as an additional perturbation and give rise to localization diagrams. Based on the obtained local orbitals,
an effective Bloch Hamiltonian is constructed to second order of perturbation theory with all third-order localization diagrams
included. In addition, the summation of certain classes of diagrams up to infinite order in the off-diagonal Fock elements
as well as the Epstein-Nesbet partitioning of the full Hamiltonian are discussed. The problem of intruder states, frequently
encountered in many-body perturbation theory, is dealt with by employing the theory of intermediate Hamiltonians. As model
systems we have chosen cyclic periodic structures up to an oligoethylene ring in double-zeta basis; however, the theory presented
here straightforwardly carries over to infinite periodic systems.
Received: 30 April 1998 / Accepted: 27 July 1998 / Published online: 7 October 1998 相似文献
13.
M. Micov L. Turi Nagy D. Tunega M. Liška P. Perichta 《Theoretical chemistry accounts》1998,99(6):378-383
A method of solvation energy computation is proposed for ions and molecules in the environment of an ionic melt, based on
the approximation of the ionic melt as an ideal conductor. The method is used to compute equilibrium constants of some equilibria
in cryolite melt. Theoretically obtained results predict that aluminium is bound in tetrafluorocomplexes AlF4
−.
Received: 16 March 1998 / Accepted: 19 June 1998 / Published online: 7 October 1998 相似文献
14.
The effects of the amino acid side chains of the binding pocket of bacteriorhodopsin (bR) and of a water molecule on the
structure of the retinal Schiff base have been studied using Becke3LYP/6-31G* level of density functional theory. A model
protonated Schiff base structure including six conjugated double bonds and methyl substituents was optimized in the presence
of several amino acid side chains and of a water molecule, separately. The Schiff base structure was also calculated in the
form of a neutral species. At each optimized complex geometry the atomic charges of the model Schiff base were calculated
using Mulliken population analysis. In agreement with previously proposed counterion(s) of the protonated retinal Schiff base
in bR, the results show that Asp85 and Asp212, which are present in the form of negatively charged groups, have significantly large effects on the structure and electronic
configuration of both unprotonated and protonated model Schiff bases. The presence of a water molecule in the vicinity of
the Schiff base demonstrates significant effects which are comparable to those of aspartate groups. Other side chains studied
did not show any significant effect in this direction. Apart from the aspartate groups and the water molecule, in none of
the other complexes studied are the atomic charges and the bond alternation of the model Schiff base significantly influenced
by the presence of the neighboring amino acids.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998 相似文献
15.
One of the purposes of studying protein stability changes upon mutations is to get information about the dominating interactions
that drive folding and stabilise the native structure. With this in mind, we present a method that predicts folding free-energy
variations caused by point mutations using combinations of two types of database-derived potentials, i.e. backbone torsion-angle
potentials and distance potentials, describing local and non-local interactions along the chain, respectively. The method
is applied to evaluate the folding free-energy changes of 344 single-site mutations introduced in six different proteins and
a synthetic peptide. We found that the relative importance of local versus non-local interactions along the chain is essentially
a function of the solvent accessibility of the mutated residues. For the subset of totally buried residues, the optimal potential
is the sum of a distance potential and a torsion potential weighted by a factor of 0.4. This combination yields a correlation
coefficient between measured and computed changes in folding free energy of 0.80. For mutations of partially buried residues,
the best potential is the sum of a torsion potential and a distance potential weighted by 0.7. For fully accessible residues,
the torsion potentials taken alone perform best, reaching correlation coefficients of 0.87 on all but 10 mutations; the excluded
mutations seem to modify the backbone structure or to involve interactions that are atypical for the surface. These results
show that the relative weight of non-local interactions along the sequence decreases as the solvent accessibility of the mutated
residue increases, and vanishes at the protein surface. On the contrary, the weight of local interactions increases with solvent
accessibility. The latter interactions are nevertheless never negligible, even for the most buried residues.
Received: 20 May 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998 相似文献
16.
The rational function optimization algorithm is one of the widely used methods to search stationary points on surfaces. However,
one of the drawbacks of this method is the step reduction procedure to deal with the overstepping problem. We present and
comment on a method such that the step obtained from the solution of the rational function equations possesses the desired
correct length. The analysis and discussion of the method is mainly centered on the location and optimization of transition
states.
Received: 18 June 1998 / Accepted: 17 September 1998 / Published online: 23 November 1998 相似文献
17.
Jaisson S Gorisse L Pietrement C Gillery P 《Analytical and bioanalytical chemistry》2012,402(4):1635-1641
Homocitrulline (HCit), an amino acid formed by the carbamylation of ε-amino groups of lysine residues, is considered a promising
biomarker for monitoring diseases such as chronic renal failure and atherosclerosis. This paper describes a tandem mass spectrometric
method for total, protein-bound and free HCit measurement in plasma samples. HCit was separated from other plasma components
by hydrophilic interaction liquid chromatography. Detection was achieved by monitoring transitions of 190.1 > 127.1 and 190.1 > 173.1
for HCit, and 183.1 > 120.2 for d7-citrulline used as internal standard. This method allowed HCit quantification within 5.2 min and was precise (inter-assay
CV < 5.85%), accurate (mean recoveries ranging from 97% to 106%), and exhibited a good linearity from 10 nmol/L to 1.6 μmol/L.
Plasma samples from control and uremic mice (n = 10) were analyzed. In control mice, mean total plasma HCit concentration was 0.78 ± 0.12 μmol/mol amino acids, whereas
it was increased 2.7-fold in uremic mice plasma, reaching 2.10 ± 0.50 μmol/mol amino acids (p < 0.001). In conclusion, this method exhibits good analytical performances and meets the criteria of sensitivity suitable
for HCit concentration assessment in plasma samples. 相似文献
18.
Elicitins are small proteins that are secreted by plant pathogenic fungi. In this work we have used a computer program that
utilizes the boundary element method for heterogeneous dielectrics with ionic strength to calculate the pK
a of all titrating groups in the 98-residue protein β-cryptogein. Our results are in reasonable agreement with the experimentally determined pK
a values for the Tyr residues in the protein. We find that the functionally important Lys13 residue has a normal pK
a of 10.3. Our work also shows that there is no direct correlation between the exposure of an amino acid sidechain and its
pK
a.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 11 November 1998 相似文献
19.
The accuracy of employing effective core polarization potentials (CPPs) to account for the effects of core-valence correlation
on the spectroscopic constants and dissociation energies of the molecules B2, C2, N2, O2, F2, CO, CN, CH, HF, and C2H2 has been investigated by comparison to accurate all-electron benchmark calculations. The results obtained from the calculations
employing CPPs were surprisingly accurate in every case studied, reducing the errors in the calculated valence D
e values from a maximum of nearly 2.5 kcal/mol to just 0.3 kcal/mol. The effects of enlarging the basis set and using higher-order
valence electron correlation treatments were found to have only a small influence on the core-valence correlation effect predicted
by the CPPs. Thus, to accurately recover the effects of intershell correlation, effective core polarization potentials such
as the ones used in the present work provide an attractive alternative to carrying out computationally demanding calculations
where the core electrons are explicitly included in the correlation treatment.
Received: 11 May 1998 / Accepted: 27 July 1998 / Published online: 28 October 1998 相似文献
20.
Subduction of Q-conjugacy representations and characteristic monomials for combinatorial enumeration
Shinsaku Fujita 《Theoretical chemistry accounts》1998,99(4):224-230
A new method of combinatorial enumeration is presented. The subduction of Q-conjugacy representations gives a characteristic subduction table and a characteristic monomial table. A cycle index is defined
on the basis of such monomials and used for combinatorial enumeration of isomers.
Received: 10 October 1997 / Accepted: 13 February 1998 / Published online: 17 June 1998 相似文献