Jeffrey L. Tilson

Domain-Based Identification and Analysis of Glutamate Receptor Ion Channels and Their Relatives in Prokaryotes

Voltage-gated and ligand-gated ion channels are used in eukaryotic organisms for the purpose of electrochemical signaling. There are prokaryotic homologues to major eukaryotic channels of these sorts, including voltage-gated sodium, potassium, and calcium channels, Ach-receptor and glutamate-receptor channels. The prokaryotic homologues have been less well characterized functionally than their eukaryotic counterparts. In this study we identify likely prokaryotic functional counterparts of eukaryotic glutamate receptor channels by comprehensive analysis of the prokaryotic sequences in the context of known functional domains present in the eukaryotic members of this family. In particular, we searched the nonredundant protein database for all proteins containing the following motif: the two sections of the extracellular glutamate binding domain flanking two transmembrane helices. We discovered 100 prokaryotic sequences containing this motif, with a wide variety of functional annotations. Two groups within this family have the same topology as eukaryotic glutamate receptor channels. Group 1 has a potassium-like selectivity filter. Group 2 is most closely related to eukaryotic glutamate receptor channels. We present analysis of the functional domain architecture for the group of 100, a putative phylogenetic tree, comparison of the protein phylogeny with the corresponding species phylogeny, consideration of the distribution of these proteins among classes of prokaryotes, and orthologous relationships between prokaryotic and human glutamate receptor channels. We introduce a construct called the Evolutionary Domain Network, which represents a putative pathway of domain rearrangements underlying the domain composition of present channels. We believe that scientists interested in ion channels in general, and ligand-gated ion channels in particular, will be interested in this work. The work should also be of interest to bioinformatics researchers who are interested in the use of functional domain-based analysis in evolutionary and functional discovery.

An ab initio study of the f–f spectroscopy of americium +3

The levels associated with the lowest 7F and 5D terms of Am+3 have been calculated using ab initio spin–orbit configuration interaction techniques. A series of configuration interaction calculations were carried out that include significant amounts of single and double excitations and with two different pseudopotentials available in the literature. Double and single excitations from the 6s, 6p, and 5f subshells are all important in the determination of the level energies. A comparison of the two examined pseudopotentials with increasing amounts of electron correlation indicates that both yield results in qualitative agreement with experiment. More importantly, though, it is estimated that both are in significant quantitative error relative to experimental results, even for very large configuration interaction calculations. The calculations were performed using the new parallel spin–orbit configuration interaction component to the COLUMBUS Program System.

Ab initio determination of americium ionization potentials

The first three ionization potentials of americium are calculated using ab initio spin–orbit configuration interaction techniques. These results are favorably compared to available experimental and previous theoretical work. The lowest two ionization potentials are accurately determined using wave functions constructed as simple single and double substitutions from a self-consistent field reference configuration with scalar relativistic effects included through an averaged relativistic pseudopotential. A determination of the third ionization potential to comparable accuracy requires inclusion of the spin–orbit operator and significant intermediate coupling with a resulting configuration expansion length in excess of 1.9 million double-group adapted functions. The solution to this problem was achieved by application of a new parallel spin–orbit configuration interaction component to the COLUMBUS Program System. A decomposition of the ionization potential calculation into parts either sensitive or largely insensitive to the spin–orbit operator is favorably tested, leading to hybrid calculations of improved accuracy.

Identifying bacterial and archaeal homologs of pentameric ligand-gated ion channel (pLGIC) family using domain-based and alignment-based approaches.

Identification of bacterial and archaeal counterparts to eukaryotic ion channels has greatly facilitated studies of structural biophysics of the channels. Often, searches based only on sequence alignment tools are inadequate for discovering such distant bacterial and archaeal counterparts. We address the discovery of bacterial and archaeal members of the Pentameric Ligand-Gated Ion Channel (pLGIC) family by a combination of four computational methods. One domain-based method involves retrieval of proteins with pLGIC-relevant domains by matching those domains to previously established domain templates in the InterPro family of databases. The second domain-based method involves searches using ungapped de-novo motifs discovered by MEME which were trained with well characterized members of the pLGIC family. The third and fourth methods involve the use of two sequence alignment search algorithms BLASTp and psiBLAST respectively. The sequences returned from all methods were screened by having the correct topology for pLGICs, and by returning an annotated member of this family as one of the first ten hits using BLASTp against a comprehensive database of eukaryotic proteins. We found the domain based searches to have high specificity but low sensitivity, while the sequence alignment methods have higher sensitivity but lower specificity. The four methods together discovered 69 putative bacterial and archaeal members of the pLGIC family. We ranked and divide the 69 proteins into groups according to the similarity of their domain compositions with known eukaryotic pLGICs. One especially notable group is more closely related to eukaryotic pLGICs than to any other known protein family, and has the overall topology of pLGICs, but the functional domains they contain are sufficiently different from those found in known pLGICs that they do not score very well against the pLGIC domain templates. We conclude that multiple methods used in a coordinated fashion outperform any single method for identifying likely distant bacterial and archaeal proteins that may provide useful models for important eukaryotic channel function. We note also that the methods used here are largely standard and readily accessible. The novelty is in the effectiveness of a strategy that combines these methods for identifying bacterial and archea relatives of this family. Therefore the paper may serve as a template for a broad group of workers to reliably identify bacterial and archaeal counterparts to eukaryotic proteins.

An ab initio study of the ionization potentials and f-f spectroscopy of europium atoms and ions.

The first three ionization potentials of europium and the f–f spectroscopy of the two lowest multiplets of Eu+3 have been calculated using ab initio spin–orbit configuration interaction techniques. To accomplish this, a new averaged relativistic effective core potential has been developed which leaves only the 5s, 5p, and 4f in the valence space. A series of configuration interaction calculations were carried out up through single and partial double excitations with a double-zeta quality basis set. The computed ionization values have an absolute error of about 0.1 eV from the experimental values. The computed f–f spectroscopy for the lowest 7F multiplet of Eu+3 has a RMS error with experiment of about 100 cm−1. The computed f–f spectroscopy for the first excited 5D multiplet has a higher RMS error of about 350 cm−1. The computed center of gravity separation between the 5D–7F multiplet is underestimated by 750 cm−1. Comparisons between non-spin–orbit and spin–orbit configuration interaction calculations fo...

Understanding the “Horizontal Dimension” of Molecular Evolution to Annotate, Classify, and Discover Proteins with Functional Domains

Protein evolution proceeds by two distinct processes: 1) individual mutation and selection for adaptive mutations and 2) rearrangement of entire domains within proteins into novel combinations, producing new protein families that combine functional properties in ways that previously did not exist. Domain rearrangement poses a challenge to sequence alignment-based search methods, such as BLAST, in predicting homology since the methodology implicitly assumes that related proteins primarily differ from each other by individual mutations. Moreover, there is ample evidence that the evolutionary process has used (and continues to use) domains as building blocks, therefore, it seems fit to utilize computational, domain-based methods to reconstruct that process. A challenge and opportunity for computational biology is how to use knowledge of evolutionary domain recombination to characterize families of proteins whose evolutionary history includes such recombination, to discover novel proteins, and to infer protein-protein interactions. In this paper we review techniques and databases that exploit our growing knowledge of “horizontal” protein evolution, and suggest possible areas of future development. We illustrate the power of the domain-based methods and the possible directions of future development by a case history in progress aiming at facilitating a particular approach to understanding microbial pathogenicity.