Biomedical subjects

Aleksandras Gutmanas

Publications and source records attributed to Aleksandras Gutmanas.

5 recordsLinked to original sources

PubMed2006

Solution NMR in structural genomics.

Structural genomics (also known as structural proteomics) aims to generate accurate three-dimensional models for all folded, globular proteins and domains in the protein universe to understand the relationship between protein sequence, structure and function. NMR spectroscopy of small (<20 kDa) proteins has been used successfully within several large-scale structural genomics projects for more than six years now. Recent advances coming from traditional NMR structural biology laboratories as well as large scale centers and consortia using NMR for structural genomics promise to facilitate NMR analysis making it even a more efficient and increasingly automated procedure.

Animals↗

PubMed2005

Accuracy and robustness of three-way decomposition applied to NMR data.

Three-way decomposition is a very versatile analysis tool with applications in a variety of protein NMR fields. It has been used to extract structural data from 3D NOESYs, to determine relaxation rates in large proteins, to identify ligand binding in screening for lead compounds, and to complement non-uniformly recorded (sparse) spectra. All applications so far concerned experimental data sets; it thus remains to address questions of accuracy and robustness of the method using simulated data where the correct answer is known. Systematic tests are presented for relaxation and NOESY data sets. Mixtures of real and synthetic data are used to allow control of various parameters and comparisons with correct reference data, while working with input that is as realistic as possible. The influence of the following parameters is evaluated: signal-to-noise, overlap of signals and the use of a regularization procedure within the algorithm. The main criteria used for the evaluation are accuracy and precision. It is shown that deterioration of accuracy is indicated by internal checks such as decrease of precision. Both with relaxation data and when interpreting NOESY spectra, three-way decomposition exhibits a robust behavior in situations with severe signal overlap and/or poor signal-to-noise, e.g., by avoiding false positives in the NOE shapes of NOESY decompositions. As a complement to this study, three-way decomposition is compared to other methods that achieve the same type of results.

Algorithms↗

PubMed2004

Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes.

Four molecular dynamics simulation trajectories of complexes between the wild-type or a mutant Antennapedia homeodomain and 2 DNA sequences were generated in order to probe the mechanisms governing the specificity of DNA recognition. The starting point was published affinity measurements showing that a single protein mutation combined with a replacement of 2 base pairs yields a new high-affinity complex, whereas the other combinations, with changes on only 1 macromolecule, exhibited lower affinity. The simulations of the 4 complexes yielded fluctuating networks of interaction. On average, these networks differ significantly, explaining the switch of affinity caused by the alterations in the macromolecules. The network of mostly hydrogen-bonding interactions involving several water molecules, which was suggested both by X-ray and NMR structures of the wild-type homeodomain and its DNA operator sequence, could be reproduced in the trajectory. More interestingly, the high-affinity complex with alterations in both the protein and the DNA yielded again a dynamic but very tight network of intermolecular interactions, however, attributing a significantly stronger role to direct hydrophobic interactions at the expense of water bridges. The other 2 homeodomain-DNA complexes, with only 1 molecule altered, show on average over the trajectories a clearly reduced number of protein-DNA interactions. The observations from these simulations suggest specific experiments and thus close the circle formed by biochemical, structural, and computational studies. The shift from a water-dominated to a more "dry" interface may prove important in the design of proteins binding DNA in a specific manner.

Antennapedia Homeodomain Protein↗

PubMed2004

Accurate relaxation parameters for large proteins.

The practical applicability, performance, and robustness of three-way decomposition (TWD) for the extraction of relaxation parameters are demonstrated for a large protein with 370 residues, the maltose binding protein. An ordinary set of seven relaxation-modulated (15)N HSQC spectra, recorded at another site, is systematically analyzed. For all 341 assigned backbone amide groups, including 21 pairs and one group of three overlapped peaks, T1 decay values were determined. On isolated peaks, TWD extracts T1 values with systematically lower error bounds compared to conventional tools, although for these simple cases the improvements remain limited. However, in the presence of spectral artifacts, the decrease in errors can become significant, demonstrating the higher robustness of TWD. For about half of the peaks in overlapped regions, the decomposition allowed separation of the signals, yielding significantly different T1 values between overlapping signals. For the rest, similarity of the decay times for the two or three overlapping signals could be confirmed within usually low error bounds. The use of TWD thus leads to a significant increase in the number of accessible relaxation probes in large proteins. With a newly implemented graphical user interface, the application of TWD requires merely a peak list, and thus no additional effort compared to conventional approaches is needed.

Algorithms↗

PubMed2002

Three-way decomposition of a complete 3D 15N-NOESY-HSQC.

Three-way decomposition is applied for the structural analysis of a complete three-dimensional (15)N-NOESY-HSQC of the 128 residues long protein azurin. The procedure presented includes decomposition using the software MUNIN, providing an initial characterization of the complete spectrum by 355 components. This is followed by post-processing yielding a final list of 149 components, 123 of which characterize 1859 NOE peaks from backbone N-H groups. Components from three-way decomposition are defined as direct products of one-dimensional shapes along the three dimensions. Thus, a complete set of distance constraints from this spectrum is obtained by one-dimensional peak picking of the shapes along the NOE dimension. Correctness and completeness of this set of NOEs are tested for all backbone amide groups against both an independent peak picking algorithm and the three-dimensional crystal structure of azurin, and a coincidence of about 95% is observed. Automated 'demixing' of components that are 'mixed' in a complex manner due to overlap of the HN and/or (15)N frequencies is illustrated.

Azurin↗