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Abstract Background A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. Findings We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG) to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated. Conclusions CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores for false positives by ~30%, while leaving true positives unaffected. Importantly, receiver operating characteristics (ROC) curves demonstrate the high correlation between CPASS similarity scores and an accurate functional assignment. As indicated by distribution curves, scores ≥ 30% infer a functional similarity. Software URL: http://cpass.unl.edu.

The functional evolution of proteins advances through gene duplication followed by functional drift, whereas molecular evolution occurs through random mutational events. Over time, protein active‐site structures or functional epitopes remain highly conserved, which enables relationships to be inferred between distant orthologs or paralogs. In this study, we present the first functional clustering and evolutionary analysis of the RCSB Protein Data Bank (RCSB PDB) based on similarities between active‐site structures. All of the ligand‐bound proteins within the RCSB PDB were scored using our Comparison of Protein Active‐site Structures (CPASS) software and database (http://cpass.unl.edu/). Principal component analysis was then used to identify 4431 representative structures to construct a phylogenetic tree based on the CPASS comparative scores (http://itol.embl.de/shared/jcatazaro). The resulting phylogenetic tree identified a sequential, step‐wise evolution of protein active‐sites and provides novel insights into the emergence of protein function or changes in substrate specificity based on subtle changes in geometry and amino acid composition. [ABSTRACT FROM AUTHOR]

ABSTRACT Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5′-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. Proteins 2014; 82:2597-2608. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The magnetic Aharonov-Bohm (A-B) effect occurs when a point charge interacts with a line of magnetic flux, while its reciprocal, the Aharonov-Casher (A-C) effect, occurs when a magnetic moment interacts with a line of charge. For the two interacting parts of these physical systems, the equations of motion are discussed in this paper. The generally accepted claim is that both parts of these systems do not accelerate, while Boyer has claimed that both parts of these systems do accelerate. Using the Euler-Lagrange equations we predict that in the case of unconstrained motion, only one part of each system accelerates, while momentum remains conserved. This prediction requires a time-dependent electromagnetic momentum. For our analysis of unconstrained motion, the A-B effects are then examples of the Feynman paradox. In the case of constrained motion, the Euler-Lagrange equations give no forces, in agreement with the generally accepted analysis. The quantum mechanical A-B and A-C phase shifts are independent of the treatment of constraint. Nevertheless, experimental testing of the above ideas and further understanding of the A-B effects that are central to both quantum mechanics and electromagnetism could be possible. [ABSTRACT FROM AUTHOR]

In 1985, Matteucci and Pozzi (1985 Phys. Rev. Lett. 54 2469) demonstrated the presence of a quantum mechanical phase shift for electrons passing a pair of oppositely charged biprism wires. For this experimental arrangement no forces deflect the electrons. Consequently, the result was reported as a non-local type-2 Aharonov-Bohm effect. Boyer (2002 Found. Phys. 32 41-50; 1987 Nuovo Cimento B 100 685-701) showed theoretically that the Matteucci-Pozzi effect could be associated with a time delay caused by a classical force. We present experimental data that confirm the presence of a time delay. This result is in contrast to the situation for the original magnetic Aharonov-Bohm effect. On similar theoretical grounds, Boyer has also associated classical forces and time delays with the magnetic Aharonov-Bohm effect. Recently, we reported the absence of such observable time delays. The contrast with our current work illustrates the subtle nature of Aharonov-Bohm effects. [ABSTRACT FROM AUTHOR]

Background: A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ∼8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ∼30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. Findings: We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG) to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated. Conclusions: CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ∼ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores for false positives by ∼30%, while leaving true positives unaffected. Importantly, receiver operating characteristics (ROC) curves demonstrate the high correlation between CPASS similarity scores and an accurate functional assignment. As indicated by distribution curves, scores ≥ 30% infer a functional similarity. Software URL: http://cpass.unl.edu. [ABSTRACT FROM AUTHOR]