Biomedical subjects

Julian Lee

Publications and source records attributed to Julian Lee.

9 recordsLinked to original sources

PubMed2006

Protein folding using fragment assembly and physical energy function.

We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function. Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms. We find nativelike structures for beta proteins, suggesting that for proteins in this class, the global tertiary structures can be determined mainly by sequence-independent backbone interactions. On the other hand, for alpha proteins, nonlocal hydrophobic side-chain interaction is also required to obtain nativelike structures.

Computer Simulation↗

PubMed2006

Measures for the assessment of fuzzy predictions of protein secondary structure.

Many of the recent secondary structure prediction methods incorporate the idea of fuzzy set theory, where instead of assigning a definite secondary structure to a query residue, probability for the residue being in each of the conformational states is estimated. Moreover, continuous assignment of conformational states to the experimentally observed protein structures can be performed in order to reflect inherent flexibility. Although various measures have been developed for evaluating performances of secondary structure prediction methods, they depend only on the most probable secondary structures. They do not assess the accuracy of the probabilities produced by fuzzy prediction methods, and they cannot incorporate information contained in continuous assignments of conformational states to observed structures. Three important measures for evaluating performance of a secondary structure prediction algorithm, Q score, Segment OVerlap (SOV) measure, and the k-state correlation coefficient (Corr), are deformed into fuzzy measures F score, Fuzzy OVerlap (FOV) measure, and the fuzzy correlation coefficient (Forr), so that the new measures not only assess probabilistic outputs of fuzzy prediction methods, but also incorporate information from continuous assignments of secondary structure. As an example of application, prediction results of four fuzzy secondary structure prediction methods, PSIPRED, PROFking, SABLE, and PREDICT, are assessed using the new fuzzy measures.

Computer Simulation↗

PubMed2005

Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.

MOTIVATION: The solvent accessibility of amino acid residues plays an important role in tertiary structure prediction, especially in the absence of significant sequence similarity of a query protein to those with known structures. The prediction of solvent accessibility is less accurate than secondary structure prediction in spite of improvements in recent researches. The k-nearest neighbor method, a simple but powerful classification algorithm, has never been applied to the prediction of solvent accessibility, although it has been used frequently for the classification of biological and medical data. RESULTS: We applied the fuzzy k-nearest neighbor method to the solvent accessibility prediction, using PSI-BLAST profiles as feature vectors, and achieved high prediction accuracies. With leave-one-out cross-validation on the ASTRAL SCOP reference dataset constructed by sequence clustering, our method achieved 64.1% accuracy for a 3-state (buried/intermediate/exposed) prediction (thresholds of 9% for buried/intermediate and 36% for intermediate/exposed) and 86.7, 82.0, 79.0 and 78.5% accuracies for 2-state (buried/exposed) predictions (thresholds of each 0, 5, 16 and 25% for buried/exposed), respectively. Our method also showed slightly better accuracies than other methods by about 2-5% on the RS126 dataset and a benchmarking dataset with 229 proteins. AVAILABILITY: Program and datasets are available at http://biocom1.ssu.ac.kr/FKNNacc/ CONTACT: jul@ssu.ac.kr.

Algorithms↗

PubMed2005

Folding simulations of small proteins.

Understanding how a protein folds is a long-standing challenge in modern science. We have used an optimized atomistic model (united-residue force field) to simulate folding of small proteins of various structures: HP-36 (alpha protein), protein A (beta), 1fsd (alpha+beta), and betanova (beta). Extensive Monte Carlo folding simulations (ten independent runs with 10(9) Monte Carlo steps at a temperature) starting from non-native conformations are carried out for each protein. In all cases, proteins fold into their native-like conformations at appropriate temperatures, and glassy transitions occur at low temperatures. To investigate early folding trajectories, 200 independent runs with 10(6) Monte Carlo steps are also performed at a fixed temperature for a protein. There are a variety of possible pathways during non-equilibrium early processes (fast process, approximately 10(4) Monte Carlo steps). Finally, these pathways converge to the point unique for each protein. The convergence point of the early folding pathways can be determined only by direct folding simulations. The free energy surface, an equilibrium thermodynamic property, dictates the rest of the folding (slow process, approximately 10(8) Monte Carlo steps).

Computer Simulation↗

PubMed2005

Protein structure prediction based on fragment assembly and parameter optimization.

We propose a novel method for ab-initio prediction of protein tertiary structures based on the fragment assembly and global optimization. Fifteen residue long fragment libraries are constructed using the secondary structure prediction method PREDICT, and fragments in these libraries are assembled to generate full-length chains of a query protein. Tertiary structures of 50 to 100 conformations are obtained by minimizing an energy function for proteins, using the conformational space annealing method that enables one to sample diverse low-lying local minima of the energy. Then in order to enhance the performance of the prediction method, we optimize the linear parameters of the energy function, so that the native-like conformations become energetically more favorable than the non-native ones for proteins with known structures. We test the feasibility of the parameter optimization procedure by applying it to the training set consisting of three proteins: the 10-55 residue fragment of staphylococcal protein A (PDB ID 1bdd), a designed protein betanova, and 1fsd.

Models, Molecular↗

PubMed2004

Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing.

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is proposed. This method utilizes the secondary structure prediction information of a query sequence and the fragment assembly procedure based on global optimization. Fifteen-residue-long fragment libraries are constructed using the secondary structure prediction method PREDICT, and fragments in these libraries are assembled to generate full-length chains of a query protein. Tertiary structures of 50 to 100 conformations are obtained by minimizing an energy function for proteins, using the conformational space annealing method that enables one to sample diverse low-lying local minima of the energy. We apply PROFESY for benchmark tests to proteins with known structures to demonstrate its feasibility. In addition, we participated in CASP5 and applied PROFESY to four new-fold targets for blind prediction. The results are quite promising, despite the fact that PROFESY was in its early stages of development. In particular, PROFESY successfully provided us the best model-one structure for the target T0161.

Caspases↗

PubMed2004

Folding of small proteins using a single continuous potential.

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single continuous potential (united-residue force field). In all cases, collapse occurs at a very early stage, and proteins fold into their nativelike conformations at appropriate temperatures. We also observe that glassy transitions occur at low temperatures. The simulation results demonstrate that the folding mechanism is controlled not only by thermodynamic factors but also by kinetic factors: The way a protein folds into its native structure is also determined by the convergence point of early folding trajectories, which cannot be obtained by the free energy surface.

Biophysics↗

PubMed2004

Milk L-lactate concentration is increased during mastitis.

A study was undertaken in cattle to evaluate changes in milk L-lactate in relation to mastitis. A healthy, rear quarter of the udder of each of ten cows in mid-lactation was infused with 1000 colony-forming units (cfu) of Streptococcus uberis following an afternoon milking. Foremilk samples were taken at each milking from control and treated quarters and antibiotic treatment was applied following the onset of clinical mastitis or after 72 h. One cow did not become infected. Six quarters showed clinical symptoms of mastitis within 24-40 h and this was associated with a more than 30-fold increase in milk L-lactate (to 3.3 mM) and an increase in somatic cell count (SCC) from 4.5 x 10(3) to 1 x 10(7) cells/ml. Three cows were subclinical, with cell counts ranging from 1.5 x 10(6) to 1 x 10(7) cells/ml. In these animals, milk lactate ranged from 0.7 to 1.5 mM in the infected quarters up to 40 h post-infection, compared with less than 0.1 mM in control quarters. Milk was examined from 137 cows in mid-lactation which were known to have mastitis. Foremilk samples were taken aseptically from control and infected quarters of cows on commercial farms. Mean milk L-lactate concentrations and SCC were 0.14 +/- 0.02 mM and 1.85 +/- 0.3 x 10(5) cells/ml, respectively, in control (bacteriologically negative) samples. However, L-lactate concentrations exceeded 2.5 mM in the presence of some types of infection, the level of the lactate response being closely related to the impact of the infection on SCC. L-Lactate concentrations were relatively elevated in milk samples taken post partum, declining from 0.8 to 0.14 mM oyer the first few days of lactation. In conclusion, milk L-lactate has potential as an indicator of clinical and subclinical mastitis in dairy cows.

Animals↗

PubMed2003

Unbiased global optimization of Lennard-Jones clusters for N < or =201 using the conformational space annealing method.

We apply the conformational space annealing method to the Lennard-Jones clusters and find all known lowest energy configurations up to 201 atoms, without using extra information of the problem such as the structures of the known global energy minima. In addition, the robustness of the algorithm with respect to the randomness of initial conditions of the problem is demonstrated by ten successful independent runs up to 183 atoms. Our results indicate that this method is a general and yet efficient global optimization algorithm applicable to many systems.

Journal Article↗