Biomedical subjects

M R Betancourt

Publications and source records attributed to M R Betancourt.

5 recordsLinked to original sources

PubMed2001

Universal similarity measure for comparing protein structures.

We introduce a new variant of the root mean square distance (RMSD) for comparing protein structures whose range of values is independent of protein size. This new dimensionless measure (relative RMSD, or RRMSD) is zero between identical structures and one between structures that are as globally dissimilar as an average pair of random polypeptides of respective sizes. The RRMSD probability distribution between random polypeptides converges to a universal curve as the chain length increases. The correlation coefficients between aligned random structures are computed as a function of polypeptide size showing two characteristic lengths of 4.7 and 37 residues. These lengths mark the separation between phases of different structural order between native protein fragments. The implications for threading are discussed.

Models, Statistical↗

PubMed2001

Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement.

An improved generalized comparative modeling method, GENECOMP, for the refinement of threading models is developed and validated on the Fischer database of 68 probe-template pairs, a standard benchmark used to evaluate threading approaches. The basic idea is to perform ab initio folding using a lattice protein model, SICHO, near the template provided by the new threading algorithm PROSPECTOR. PROSPECTOR also provides predicted contacts and secondary structure for the template-aligned regions, and possibly for the unaligned regions by garnering additional information from other top-scoring threaded structures. Since the lowest-energy structure generated by the simulations is not necessarily the best structure, we employed two structure-selection protocols: distance geometry and clustering. In general, clustering is found to generate somewhat better quality structures in 38 of 68 cases. When applied to the Fischer database, the protocol does no harm and in a significant number of cases improves upon the initial threading model, sometimes dramatically. The procedure is readily automated and can be implemented on a genomic scale.

Algorithms↗

PubMed1999

Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity.

The chaperonin system, GroEL and GroES of Escherichia coli enable certain proteins to fold under conditions when spontaneous folding is prohibitively slow as to compete with other non-productive channels such as aggregation. We investigated the plausible mechanisms of GroEL-mediated folding using simple lattice models. In particular, we have investigated protein folding in a confined environment, such as those offered by the GroEL, to decipher whether rate and yield enhancement can occur when the substrate protein is allowed to fold within the cavity of the chaperonins. The GroEL cavity is modeled as a cubic box and a simple bead model is used to represent the substrate chain. We consider three distinct characteristic of the confining environment. First, the cavity is taken to be a passive Anfinsen cage in which the walls merely reduce the available conformation space. We find that at temperatures when the native conformation is stable, the folding rate is retarded in the Anfinsen cage. We then assumed that the interior of the wall is hydrophobic. In this case the folding times exhibit a complex behavior. When the strength of the interaction between the polypeptide chain and the cavity is too strong or too weak we find that the rates of folding are retarded compared to spontaneous folding. There is an optimum range of the interaction strength that enhances the rates. Thus, above this value there is an inverse correlation between the folding rates and the strength of the substrate-cavity interactions. The optimal hydrophobic walls essentially pull the kinetically trapped states which leads to a smoother the energy landscape. It is known that upon addition of ATP and GroES the interior cavity of GroEL offers a hydrophilic-like environment to the substrate protein. In order to mimic this within the context of the dynamic Anfinsen cage model, we allow for changes in the hydrophobicity of the walls of the cavity. The duration for which the walls remain hydrophobic during one cycle of ATP hydrolysis is allowed to vary. These calculations show that frequent cycling of the wall hydrophobicity can dramatically reduce the folding times and increase the yield as well under non-permissive conditions. Examination of the structures of the substrate proteins before and after the change in hydrophobicity indicates that there is global unfolding involved. In addition, it is found that a fraction of the molecules kinetically partition to the native state in accordabce with the iterative annealing mechanism. Thus, frequent "unfoldase" activity of chaperonins leading to global unfolding of the polypeptide chain results in enhancement of the folding rates and yield of the folded protein. We suggest that chaperonin efficiency can be greatly enhanced if the cycling time is reduced. The calculations are used to interpret a few experiments on chaperonin-mediated protein folding.

Amino Acid Sequence↗

PubMed1999

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes.

We examine the similarities and differences between two widely used knowledge-based potentials, which are expressed as contact matrices (consisting of 210 elements) that gives a scale for interaction energies between the naturally occurring amino acid residues. These are the Miyazawa-Jernigan contact interaction matrix M and the potential matrix S derived by Skolnick J et al., 1997, Protein Sci 6:676-688. Although the correlation between the two matrices is good, there is a relatively large dispersion between the elements. We show that when Thr is chosen as a reference solvent within the Miyazawa and Jernigan scheme, the dispersion between the M and S matrices is reduced. The resulting interaction matrix B gives hydrophobicities that are in very good agreement with experiment. The small dispersion between the S and B matrices, which arises due to differing reference states, is shown to have dramatic effect on the predicted native states of lattice models of proteins. These findings and other arguments are used to suggest that for reliable predictions of protein structures, pairwise additive potentials are not sufficient. We also establish that optimized protein sequences can tolerate relatively large random errors in the pair potentials. We conjecture that three body interaction may be needed to predict the folds of proteins in a reliable manner.

Models, Molecular↗

PubMed1998

Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics.

BACKGROUND: The most conspicuous feature of a right-handed alpha helix is the presence of hydrogen bonds between the backbone carbonyl oxygen and NH groups along the chain. A simple off-lattice model that includes hydrogen bond interactions using virtual atoms is used to examine the stability, cooperativity and kinetics of the helix-coil transition. RESULTS: We have studied the thermodynamics (using multiple histogram method) and kinetics (by Brownian dynamics simulations) of 16-mer minimal off-lattice models of four-turn alpha-helix sequences. The carbonyl and NH groups are represented as virtual moieties located between two alpha-carbon atoms along the polypeptide chain. The characteristics of the native conformations of the model helices, such as the helical pitch and angular correlations, coincide with those found in real proteins. The transition from coil to helix is quite broad, which is typical of these finite-sized systems. The cooperativity, as measured by a dimensionless parameter, omegac, that takes into account the width and the slope of the transition curves, is enhanced when hydrogen bonds are taken into account. The value of omegac for our model is consistent with that inferred from experiment for an alanine-based helix-forming peptide. The folding time tauF ranges from 6 to 1000 ns in the temperature range 0.7-1.9 T(F), where T(F) is the helix-coil transition temperature. These values are in excellent agreement with the results from recent fast folding experiments. The temperature dependence of tauF exhibits a nearly Arrhenius behavior. Thermally induced unfolding occurs on a time scale that is less than 40-170 ps depending on the final temperature. Our calculations also predict that, although tauF can be altered by changes in the sequence, the dynamic range over which such changes take place is not as large as that predicted for beta-turn formation. CONCLUSIONS: Hydrogen bonds not only affect the stability of alpha-helix formation but also have profound influence on the kinetics. The excellent agreement between our calculations and experiments suggests that these models can be used to investigate the effects of sequence, temperature and viscosity on the helix-coil transition.

Animals↗