A P2 and P3 substrate specificity comparison between the Murray Valley encephalitis and West Nile virus NS2B/NS3 protease using C-terminal agmatine dipeptides

The Murray Valley encephalitis virus (MVEV) and the West Nile virus (WNV) are mosquito-borne single-stranded RNA Flaviviruses responsible for many cases of viral encephalitis and deaths worldwide. The former is endemic in north Australia and Papua New Guinea while the latter has spread to different parts of the world and was responsible for a recent North American outbreak in 2012, resulting in 243 fatalities. There is currently no approved vaccines or drugs against MVEV and WNV viral infections. A plausible drug target is the viral non-structural NS2B/NS3 protease due to its role in viral replication. This trypsin-like serine protease recognizes and cleaves viral polyproteins at the C-terminal end of an arginine residue, opening an avenue for the development of peptide-based antivirals. This communication compares the P2 and P3 residue preferences of the MVEV and WNV NS2B/NS3 proteases using a series of C-terminal agmatine dipeptides. Our results revealed that both viral enzymes were highly specific toward lysines at the P2 and P3 positions, suggesting that a peptidomimetic viral protease inhibitor developed against one virus should also be active against the other.

NMR analysis of a novel enzymatically active unlinked dengue NS2B-NS3 protease complex

The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a two-component trypsin-like protease that contains the cofactor region from the nonstructural protein NS2B and the protease domain from NS3 (NS3pro). The NS2B-NS3pro complex plays a crucial role in viral maturation and has been identified as a potential drug target. Using a DENV protease construct containing NS2B covalently linked to NS3pro via a Gly4-Ser-Gly4 linker ("linked protease"), previous x-ray crystal structures show that the C-terminal fragment of NS2B is remote from NS3pro and exists in an open state in the absence of an inhibitor; however, in the presence of an inhibitor, NS2B complexes with NS3pro to form a closed state. This linked enzyme produced NMR spectra with severe signal overlap and line broadening. To obtain a protease construct with a resolved NMR spectrum, we expressed and purified an unlinked protease complex containing a 50-residue segment of the NS2B cofactor region and NS3pro without the glycine linker using a coexpression system. This unlinked protease complex was catalytically active at neutral pH in the absence of glycerol and produced dispersed cross-peaks in a (1)H-(15)N heteronuclear single quantum correlation spectrum that enabled us to conduct backbone assignments using conventional techniques. In addition, titration with an active-site peptide aldehyde inhibitor and paramagnetic relaxation enhancement studies demonstrated that the unlinked DENV protease exists predominantly in a closed conformation in solution. This protease complex can serve as a useful tool for drug discovery against DENV.

Exploring the binding of peptidic West Nile virus NS2B-NS3 protease inhibitors by NMR

West Nile virus (WNV) NS2B-NS3 protease is an important drug target since it is an essential protein for the replication of the virus. In order to determine the minimum pharmacophore for protease inhibition, a series of dipeptide aldehydes were synthesized. The 50% inhibitory concentration (IC(50)) measurements revealed that a simple acetyl-KR-aldehyde was only threefold less active than 4-phenyl-phenylacetyl-KKR-aldehyde (1) (Stoermer et al., 2008) that was used as the reference compound. The ligand efficiency of 0.40 kcal/mol/HA (HA=heavy atom) for acetyl-KR-aldehyde is much improved compared to the reference compound 1 (0.23 kcal/mol/HA). The binding of the inhibitors was examined using (1)H-(15)N-HSQC experiments and differential chemical shifts were used to map the ligand binding sites. The biophysical studies show that the conformational mobility of WNV protease has a major impact on the design of novel inhibitors, since the protein conformation changes profoundly depending on the structure of the bound ligand.

Commercial porters of eastern Nepal: health status, physical work capacity, and energy expenditure

The purpose of the study was to compare full-time hill porters in eastern Nepal with part-time casual porters engaged primarily in subsistence farming. The 50 porters selected for this study in Kenja (elevation 1,664 m) were young adult males of Tibeto-Nepali origin. Following standardized interviews, anthropometry, and routine physical examinations, the porters were tested in a field laboratory for physiological parameters associated with aerobic performance. Exercise testing, using a step test and indirect calorimetry, included a submaximal assessment of economy and a maximal-effort graded exercise test. Energy expenditure was measured in the field during actual tumpline load carriage. No statistically significant differences were found between full-time and part-time porters with respect to age, anthropometric characteristics, health, nutritional status, or aerobic power. Mean VO2 peak was 2.38 +/- 0.27 L/min (47.1 +/- 5.3 ml/kg/min). Load-carrying economy did not differ significantly between porter groups. The relationship between VO2 and load was linear over the range of 10-30 kg with a slope of 9 +/- 4 ml O2/min per kg of load. During the field test of actual work performance, porters expended, on average, 348 +/- 68 kcal/hr in carrying loads on the level and 408 +/- 60 kcal/hr in carrying loads uphill. Most porters stopped every 2 min, on average, to rest their loads briefly on T-headed resting sticks (tokmas). The technique of self-paced, intermittent exercise together with the modest increase in energy demands for carrying increasingly heavier loads allows these individuals to regulate work intensity and carry extremely heavy loads without creating persistent medical problems.

Commercial porters of eastern Nepal: health status, physical work capacity, and energy expenditure

The purpose of the study was to compare full-time hill porters in eastern Nepal with part-time casual porters engaged primarily in subsistence farming. The 50 porters selected for this study in Kenja (elevation 1,664 m) were young adult males of Tibeto-Nepali origin. Following standardized interviews, anthropometry, and routine physical examinations, the porters were tested in a field laboratory for physiological parameters associated with aerobic performance. Exercise testing, using a step test and indirect calorimetry, included a submaximal assessment of economy and a maximal-effort graded exercise test. Energy expenditure was measured in the field during actual tumpline load carriage. No statistically significant differences were found between full-time and part-time porters with respect to age, anthropometric characteristics, health, nutritional status, or aerobic power. Mean VO2 peak was 2.38 +/- 0.27 L/min (47.1 +/- 5.3 ml/kg/min). Load-carrying economy did not differ significantly between porter groups. The relationship between VO2 and load was linear over the range of 10-30 kg with a slope of 9 +/- 4 ml O2/min per kg of load. During the field test of actual work performance, porters expended, on average, 348 +/- 68 kcal/hr in carrying loads on the level and 408 +/- 60 kcal/hr in carrying loads uphill. Most porters stopped every 2 min, on average, to rest their loads briefly on T-headed resting sticks (tokmas). The technique of self-paced, intermittent exercise together with the modest increase in energy demands for carrying increasingly heavier loads allows these individuals to regulate work intensity and carry extremely heavy loads without creating persistent medical problems.

Compression of protein sequence databases

We have created an algorithm for compressing a PIR database to assist individual researchers and software developers who utilize sequence database information but may not have huge storage space. The resulting compact databank contains compressed PIR information and an interface written in C which allows fast direct access to the stored information without extensive decompression of corresponding files. The databank files as well as the interface C-file can be used on both PC-compatibles and UNIX-based computers without any modifications. The interface supports all standard PIR Request Network queries (i.e. gets databank SEQ number by entry; for a defined databank SEQ number, gets specified information like: name, organism(s), keyword(s), sequence, sequence features with coordinates, etc.). In contrast with PIR Request Network, our package allows us to call PIR-contained information directly from the C programs, even on a personal computer not on a network. Our PIR-derived databank, SAGITTARIUS PIR, was implemented in the form of separate file sets. Each file set contains database information of independent types (i.e. sequences, entry indexes, organisms, etc.). On a particular computer, the available configuration of the PIR information (and storage space) can be easily changed as needed by the user without affecting retrievals of other types of stored information. Due to an original alignment-based algorithm, in the compression of protein sequences themselves, our package out-performs the well-known ZIP file compressor. For PC-compatibles, a dialogue shell is available which supports all standard PIR Request Network queries plus homology searches, alignments, etc.

Ancient splice junction shadows with relation to blocks in protein structure

Splice junction shadows (ancient exon-exon junctions) presumably reflect the existence of amino acid primary blocks which were used in the course of evolution for the construction of new proteins. The lengths of such blocks (i.e. regions between splice junctions), as the lengths of corresponding inserted or duplicated ancient exons, should be divisible by three in order to store the preexisting coding frame in the course of evolution. In this paper, we will test the hypothesis of intron-mediated recombination in a model of block molecular evolution (exon shuffling) by revealing corresponding blocks in existing database-contained coding sequences. For this purpose, we use a weight matrix prediction of ancient splice junction shadows in coding regions of the nucleotide sequences in current databases. The usage of splice junction shadows allows us to test the block evolution hypothesis in better detail in comparison with previous methods which were based only on currently existing recent exons. Our result of block length distribution at the nucleotide level shows a clear tendency to be divisible by three. At the protein level, several unexpected favorable block lengths, which are six, nine, 12 and 15 amino acids in length, were observed. Further refinements in our method for revealing splice junction shadows (structural block boundaries) might reveal peptides which probably maintain stable folds in different structures. The latter can in turn be used for protein structure prediction.

Analysis of peptides from known proteins: clusterization in sequence space

A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to points in the CSS. The aim was to analyze clusterization of protein sequences in the CSS and to test various hypotheses about the possible evolutionary basis of this clusterization. The authors developed an easy-to-use technique which can reveal and analyze such a clusterization in a multidimensional CSS. Application of the technique led to an unexpectedly high clusterization of points in the CSS corresponding to k-tuples from known proteins. The clusterization could not be inferred from nonuniform amino acid frequencies or be explained by the influence of homologous data. None of the tested possible evolutionary and structural factors could explain the clusterization observed either. It looked as if certain protein sequence variations occurred and were fixed in the early course of evolution. Subsequent evolution (predominantly neutral) allowed only a limited number of changes and permitted new variants which led to preservation of certain k-tuples during the course of evolution. This was consistent with the theory of exon shuffling and protein block structure evolution. Possible applications of sequence space features found were also discussed.

Data bank homology search algorithm with linear computation complexity

A new algorithm for data bank homology search is proposed. The principal advantages of the new algorithm are: (i) linear computation complexity; (ii) low memory requirements; and (iii) high sensitivity to the presence of local region homology. The algorithm first calculates indicative matrices of k-tuple 'realization' in the query sequence and then searches for an appropriate number of matching k-tuples within a narrow range in database sequences. It does not require k-tuple coordinates tabulation and in-memory placement for database sequences. The algorithm is implemented in a program for execution on PC-compatible computers and tested on PIR and GenBank databases with good results. A few modifications designed to improve the selectivity are also discussed. As an application example, the search for homology of the mouse homeotic protein HOX 3.1 is given.

VisiCoor: a simple program for visualization of proteins

A well-drawn picture acts as an excellent metaphor for something real, and human vision provides instant, random access to any part of which the picture represents. It is in this sense that pictures can convey information more effectively than words alone. The power of the graphics work-stations available today makes visual presentation of scientific results a reality. A molecular graphics program for investigating protein structures, as well as several sample plots that show the power of the program, are presented.

Generalized tube model of biased reptation for gel electrophoresis of DNA

A theoretical analysis of the reptational motion of DNA in a gel that includes the effects of molecular fluctuations has been used to explain the main features found in experiments involving periodic inversion of the electric field. The resonance-like decrease of the electrophoretic mobility as a function of pulse duration is related to transient "undershoots" in the orientation of the molecule, in agreement with recent experimental data. These features arise from a delicate interplay of internal and center of mass motion of the molecules under pulsed field conditions, and are important for the separation of DNA molecules in the size range 0.2 to 10 million base pairs.