Generalized-ensemble algorithms for molecular simulations of biopolymers.

In complex systems with many degrees of freedom such as peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems.

Electrostatic effects on the alpha-helix and beta-strand formation of BPTI(16-36) studied by Monte Carlo simulated annealing.

The electrostatic effects on the secondary structure forming tendencies of a peptide fragment with residues 16-36 of bovine pancreatic trypsin inhibitor, BPTI(16-36), are studied using Monte Carlo simulated annealing simulations. We consider three dielectric functions epsilon(r) of distance r: constant dielectric function (epsilon = 2; strong electrostatic interactions) and sigmoidal functions varying from epsilon(0) = 2 to epsilon(infinity) = 47 (intermediate) and to epsilon(infinity) = 78 (weak). Simulations with epsilon = 2 suggest that this peptide exhibits a significant propensity for beta-strand formations in accordance with a beta-sheet structure of the relevant segment in native BPTI. The tendency for alpha-helix formations becomes almost comparable with that of beta-strands in the simulation with epsilon(infinity) = 47, and there appears no appreciable conformational propensity for this case. Finally, the results with epsilon(infinity) = 78 generate low-energy conformations with conspicuous alpha-helices. These findings suggest the possibility that the change in electrostatic interactions can be the key factor for the conformational transitions of peptides between alpha-helix and beta-sheet that have recently been observed in experiments. These changes in electrostatic interactions can arise from those in various environmental factors such as conformations of the rest of the protein molecule and solvent conditions.

New Monte Carlo algorithms for protein folding.

Over the past three decades, a number of powerful simulation algorithms have been introduced to the protein folding problem. For many years, the emphasis has been placed on how to both overcome the multiple minima problem and find the conformation with the global minimum potential energy. Since the new view of the protein folding mechanism (based on the free energy landscape of the protein system) arose in the past few years, however, it is now of interest to obtain a global knowledge of the phase space, including the intermediate and denatured states of proteins. Monte Carlo methods have proved especially valuable for these purposes. As well as new, powerful optimization techniques, novel algorithms that can sample much a wider phase space than conventional methods have been established.

The folding funnel landscape for the peptide Met-enkephalin.

We study the free energy landscape of the small peptide Met-enkephalin. Our data were obtained from a generalized-ensemble Monte Carlo simulation taking the interactions among all atoms into account. We show that the free energy landscape resembles that of a funnel, indicating that this peptide is a good folder. Our work demonstrates that the energy landscape picture and folding concept, developed in the context of simplified protein models, can also be used to describe the folding in more realistic models.

Clinically applicable bulk isolation of blood CD34+ cells for autografting in children.

CD34+ cells were purified in bulk from apheresis-collected cells of children with cancer using monoclonal antibody (MoAb) and magnetic beads (Baxter ISOLEX system). To improve the purity of the final product for possibly better tumor cell purging and to make the manufacturer's original procedure more cost-effective, we incubated the cells for 30 min with l-phenylalanine methylester hydrochloride (PME) to reduce the cell number by removing contaminating granulocytes and monocytes in the initial step before incubation with MoAb. Our modification prevented nonspecific interactions between MoAb and magnetic beads, and thereby saved expensive materials for purification. A total of 40 purifications were performed with samples containing a mean of 3.1 x 10(9) blood cells mobilized from 15 children by chemotherapy plus granulocyte colony-stimulating factor (G-CSF). The entire purification procedure, from the end of apheresis to storage, was completed within 5h. After incubation with PME and double-layered (40/60%) Percoll separation, the number of CD34+ cells was reduced to 48+/-29%, which suggests the possibility that half of the CD34+ cells in the inoculum were nonclonogenic in the hematopoietic progenitor assay. PME/Percoll-treated cells were then subjected to a final isolation procedure with MoAb according to the manufacturer's suggestions, and 52+/-42% and 32+/-22%, respectively, of the CFU-GM and CD34+ cells present in the initial bag inoculums were recovered. The recovery rates were, respectively, 54% and 67%, when the calculation was limited to the isolation procedure with MNoAb. The purity of isolated CD34+ cells and the plating efficiency in methylcellulose culture were, respectively, 77+/-24% and 33+/-13%. Fourteen children were subsequently autografted with purified CD34+ cells after marrow ablative chemotherapy. The median number of days to achieve an ANC of 0.5 x 10(9)/l was 12 and that to achieve a platelet count of 50 x 10(9)/l was 22.5, which were comparable to those in our historical group of 55 patients who underwent transplant with unmanipulated blood cells (13 and 16 days). These results suggest that our modified purification procedure with PME is useful for the initial reduction of cell numbers to save costly materials, and that cells isolated by this procedure can be directly used in clinical transplantation procedures.

Temperature dependence of distributions of conformations of a small peptide.

Multicanonical Monte Carlo simulations of the pentapeptide Met-enkephalin were used to study its low-energy conformations in detail. The resulting conformations are classified into six categories of similar structures based on the pattern of intrachain hydrogen bonds. Several thermodynamic quantities such as the distributions of hydrogen bonds and those of backbone dihedral angles were obtained as a function of temperature. From these results, it was concluded that at least four of the six categories are well-defined local minimum energy states. These four categories are in agreement with our prior results based on root-mean-square interatomic distances.

[Clinical benefit of nutritional assessment and support in patients with chronic obstructive pulmonary disease].

Weight loss is common in patients with chronic obstructive pulmonary disease (COPD). Comprehensive nutritional assessment was conducted in two large groups of patients with COPD who were enrolled in the Respiratory Failure Research Program sponsored by the Japanese Ministry of Health and Welfare and the Kinki COPD Research Group. The incidences of mild malnutrition (%IBW < 90%) were 74% and 62%, respectively. The incidences of hypoalbuminemia were low: 10.0% and 6.5%, respectively. The incidence of imbalance in plasma amino acids, which was defined as an abnormally low BCAA/AAA ratio, was as high as 93% in patients with COPD and chronic respiratory failure. The %IBW was significantly related to the FEV1 and to the DLco/VA. The moderately-malnourished subpopulation was characterized by a greater degree of hyperinflation and hypercapnea: the measured resting energy expenditure (REE) was significantly higher than the values in age-matched healthy controls. REE/REEpred was significantly and inversely related to BCAA/AAA and to Pimax. REE was inversely related to FEV1%. REE in the subgroup with severe hyperinflation was significantly higher than REE in those with milder hyperinflation. Among patients with an FEV1% of less than 50%, mortality tended to be higher in those with lower body weight, and this relationship was stronger in patients with an FEV1% of more than 50%. When patients were given a BCAA-enriched enteral formula in addition to their usual diet for 3 months, there was a significant increase in body weight, transferrin level, and Pimax.

Helix-forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing.

Monte Carlo simulated annealing is applied to the study of the alpha-helix-forming tendencies of seven nonpolar amino acids, Ala, Leu, Met, Phe, Ile, Val, and Gly. Homooligomers of 10 amino acids are used and the helix tendency is calculated by folding alpha-helicies from completely random initial conformations. The results of the simulation imply that Met, Ala, and Leu are helix formers and that Val, Ile, and Gly are helix breakers, while Phe comes in between the two groups. The differences between helix formers and breakers turned out to be large in agreement with the recent experiments with short peptides. It is argued from the energy distributions of the obtained conformations that the helix tendency is small for the helix breakers because of steric hindrance of side chains. Homoglycine is shown to favor a random coil conformation. The beta-strand tendencies of the same homooligomers are also considered, and they are shown to agree with the frequencies of amino acids in beta-sheet from the protein data base.

Dependence on the dielectric model and pH in a synthetic helical peptide studied by Monte Carlo simulated annealing.

Monte Carlo simulated annealing is applied to the tertiary structure prediction of a 17-residue synthetic peptide, which is known by experiment to exhibit high helical content at low pH. Two dielectric models are considered: sigmoidal distance-dependent dielectric function and a constant dielectric function (epsilon = 2). Starting from completely random initial conformations, our simulations for both dielectric models at low pH gave many helical conformations. The obtained low-energy conformations are compared with the nuclear Overhauser effect spectroscopy cross-peak data for both main chain and side chains, and it is shown that the results for the sigmoidal dielectric function are in remarkable agreement with the experimental data. The results predict the existence of two disjoint helices around residues 5-9 and 11-16, while nmr experiments imply significant alpha-helix content between residues 5 and 14. Simulations with high pH, on the other hand, hardly gave a helical conformation, which is also in accord with the experiment. These findings indicate that when side chains are charged, electrostatic interactions due to these changes play a major role in the helix stability. Our results are compared with the previous 500 ps molecular dynamics simulations of the same peptide. It is argued that simulated annealing is superior to molecular dynamics in two respects: (1) direct folding of alpha-helix from completely random initial conformations is possible for the former, whereas only unfolding of an alpha-helix can be studied by the latter; (2) while both methods predict high helix content for low pH, the results for high pH agree with experiment (low helix content) only for the former method.

Alpha-helix structure of parathyroid hormone fragment (1-34) predicted by Monte Carlo simulated annealing.

Tertiary structure of parathyroid hormone fragment (1-34) is predicted by the Monte Carlo simulated annealing method. Among the 20 structures obtained after completely unbiased calculations, the lowest-energy conformation exhibits two alpha-helices around residues 2-10 and 18-22. This structure agrees with the models, especially with the location of helices, deduced from experiments. In addition, the simulation supports empirical implications in the following two points. (1) The helix near the N-terminus is more stable than the C-terminal one. (2) The rest of the peptide segments are flexible and do not tend to have any definite structure. Our calculation correctly predicts only an alpha-helix, whereas previous analyses by the Chou-Fasman method leave an ambiguity between an alpha-helix and a beta-strand.

[Quantitative assessment of fibroblast viability in cryopreserved aortic valve allografts].

The purpose of this study is to clarify whether serum (fetal bovine serum or human serum) is necessary or not for cryopreservation of aortic valve allografts. The protective effects of fetal bovine serum compared with human serum were evaluated by means of quantitative assessment of fibroblast viability. Porcine aortic valves were excised and rinsed immediately after death, followed by treatment with low concentration antibiotics. Valves were gradually frozen at a control-rate of -1 degree C/min and then stored in liquid nitrogen vapor-phase. The samples were classified into three groups by nutrient medium as follows. Group A (n = 5); Dulbecco's Modified Eagle Medium (DMEM), Group B (n = 5); DMEM containing 10% fetal bovine serum, Group C (n = 5); DMEM containing 20% human serum. At 1 week, 1 month, and 3 months after initiation of storage, the valves were thawed rapidly and examined for fibroblast viability, which was assessed quantitatively by means of autoradiography with tritiated proline. After 1 week storage, the fibroblast viability rate reduced from 98% to 80.7% in group A, 79.4% in group B and 79.2% in group C respectively, but there were no significant differences among three groups. The viability rate decreased with the passage of time, and remained around 72% in all groups after 3 months storage. The histological examination did not show any changes in the structure of the valves in all samples up to 3 months of storage. The results demonstrate that the fibroblasts are still viable after 3 months storage by cryopreservation. The addition of fetal bovine serum or human serum does not improve fibroblast viability.(ABSTRACT TRUNCATED AT 250 WORDS)

Beta-sheet folding of fragment (16-36) of bovine pancreatic trypsin inhibitor as predicted by Monte Carlo simulated annealing.

A tertiary structure prediction is described using Monte Carlo simulated annealing for the peptide fragment corresponding to residues 16-36 of bovine pancreatic trypsin inhibitor (BPTI). The simulation starts with randomly chosen initial conformations and is performed without imposing experimental constraints using energy functions given for generic interatomic interactions. Out of 20 simulation trials, seven conformations show a sheet-like structure--two strands connected by a turn--although this sheet-like structure is not as rigid as that observed in native BPTI. It is also shown that these conformations are mostly looped and exhibit a native-like right-handed twist. Unlike the case with the C-peptide of RNase A, no conspicuous alpha-helical structure is found in any of the final conformations obtained in the simulation. However, the lowest-energy conformation does not resemble exactly the native structure. This indicates that the rigid beta-sheet conformation of native BPTI merely corresponds to a local minimum of the energy function if the fragment with residues 16-36 is isolated from the native protein. A statistical analysis of all 20 final conformations suggests that the tendency for the peptide segments to form extended beta-strands is strong for those with residues 18-24, and moderate for those with residues 30-35. The segment of residues 25-29 does not tend to form any definite structure. In native BPTI, the former segments are involved in the beta-sheet and the latter in the turn. A folding scenario is also speculated from this analysis.

Alpha-helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A.

Conformation of the C-peptide fragment of RNase A is calculated by Monte Carlo simulated annealing. We adopt the total potential energy as given by the sum of generic interatomic energies whose parameters are determined separately for each amino acid without referring to the empirical structure of the C-peptide. The simulation is carried out in a completely unrestricted way without imposing any weight towards given final destinations. Starting from completely random initial conformations and minimizing the total potential energy with respect to main-chain dihedral angles and side-chain torsion angles, we have obtained partial alpha-helix structure with a high probability (approximately 40%). The energetically most favourable structure exhibits a 2.5-turn alpha-helix at the location identical with that of the 3-turn alpha-helix in the native enzyme molecule. Classification of conformations obtained in the simulation into clusters of similar structure shows that our simulation indeed predicts the alpha-helix structure for the isolated C-peptide with specific charged residues. The results of simulation with various amino acid substitutions are also found to be consistent with the experimental implication for the importance of intramolecular ionic interactions for alpha-helix stability for this peptide.

A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method.

The Monte Carlo simulated annealing method has been applied to the prediction of three-dimensional structures of enkephalin. The low-energy conformations obtained were classified into a few groups of similar structures, which indicates that our method is effective. New low-energy structures were identified together with previously proposed structures.

Myocardial positron tomography with N-13 ammonia in assessment of aortocoronary bypass surgery.

A total of 20 patients were examined at rest and during stress with N-13-ammonia myocardial positron emission tomography (PET) before and after aortocoronary bypass surgery in an attempt to evaluate the effect of surgery on myocardial perfusion and to predict the graft status. The PET images were divided into anterior, septal, apical, lateral and posteroinferior segments for analysis and were evaluated as "normal" (no perfusion defects during stress and at rest), "ischemia" (stress-induced defects) and "fibrosis" (persistent defects both at rest and during stress). Approximately 90% of the segments which were ischemic before surgery became normal after surgery. Thus, ischemic changes are highly reversible, and the vessels perfusing these ischemic areas are most suitable for bypass surgery. However, most of the persistent defects failed to respond to revascularization surgery and, hence, represented irreversibly damaged myocardium. In predicting graft status, graft patency could be demonstrated by normal perfusion in postoperative images (p less than 0.01) or by improved perfusion when pre- and postoperative images were compared (p less than 0.01). However, graft occlusion could not be predicted reliably. This study demonstrated that PET with N-13 ammonia was useful in the assessment of the effects of aortocoronary bypass surgery. However, this technique was not significantly superior to thallium-201 single-photon emission computed tomography for only qualitative analysis.