Search PubMed⌕ Search

Biomedical subjects

W P Hu

Publications and source records attributed to W P Hu.

11 recordsLinked to original sources
PubMed2005

Immunodetection of pentamer and modified C-reactive protein using surface plasmon resonance biosensing.

In clinical practices, the examination of pentamer C-reactive protein (pCRP) is commonly used as a prognostic indicator of the risk of a patient developing cardiovascular disease (CVD). Structural modification of pCRP produces a modified CRP (mCRP) which exhibits different biological activities in the body. In recent years, mCRP has come to be regarded as a more powerful inducer than pCRP, and hence mCRP measurement has emerged as an important indicator for assessing the risk of developing CVD. The surface plasmon resonance (SPR) biosensing technique can be employed to increase the detection accuracy and real-time response when sensing pCRP or mCRP. In this study, three monoclonal antibodies (Mabs), C8, 8D8, and 9C9, are immobilized on a protein G layer for subsequent CRP detection. The experimental results reveal that the Mab C8 reacts with both pCRP and mCRP, the Mab 8D8 with pCRP, and the Mab 9C9 with mCRP. No false signals caused by non-specific binding are observed. When detecting pCRP using Mab C8, the SPR bioassay provides sufficient sensitivity to evaluate whether or not a patient is at risk of developing CVD. SPR biosensing provides a viable and accurate approach for the real-time evaluation of pCRP and mCRP levels, and is therefore of considerable benefit in clinical examinations of CPR.

Antibodies, Monoclonal↗
PubMed2005

Differential expression of splice variant and wild-type parkin in sporadic Parkinson's disease.

BACKGROUND: Altered splicing of parkin under cellular stress could lead to changes in gene expression and altered protein activity. The causative role of parkin in sporadic Parkinson's disease (PD) is unknown. OBJECTIVES: We described a parkin splice variant (SV) in the substantia nigra and leukocytes of sporadic PD patients. Using a case control methodology, we investigated the exon 4 SV (E4SV) and wild-type parkin expression in the leukocytes of sporadic PD patients and healthy individuals. METHODS/RESULTS: We identified a parkin E4SV in the substantia nigra and leukocytes of sporadic PD patients and controls by reverse transcriptase-polymerase chain reaction (PCR). The exon 4 (122 bp) deletion resulted in a reading frame shift over the junction of exons 3-5 and a stop codon (tga) 17 bp downstream from exon 3. The translated truncated protein was associated with a total loss of the two-RING finger functional domain. Utilizing TaqMan real-time PCR with probes located across the junction of exons 3-4 or 3-5, we demonstrated an over-expression of E4SV/wild-type parkin ratio in the leukocytes of sporadic PD patients compared to age-, gender-, and race-matched controls (p<0.0005). A multivariate regression analysis demonstrated that the ratio of E4SV/wild-type parkin expression increased with age in PD patients, but this was not observed in the controls (p<0.0005). CONCLUSION: The relative expression of E4SV/wild type parkin was increased in sporadic PD compared to healthy controls. Based on our observations, further functional studies to determine the pathophysiologic role of E4SV in sporadic PD patients will be of importance.

Aged↗
PubMed2004

A novel ultrahigh-resolution surface plasmon resonance biosensor with an Au nanocluster-embedded dielectric film.

The detection performance of conventional surface plasmon resonance (SPR) biosensors is limited to a 1 pg/mm(2) surface coverage of biomolecules, and consequently, such sensors struggle to detect the interaction of small molecules in low concentrations. The present study is attempted to propose the use of a novel SPR biosensor with Au nanoclusters embedded in a dielectric film to achieve a 10-fold improvement in the resolution performance. A co-sputtering method utilizing a multi-target sputtering system is used to fabricate the present dielectric films (SiO(2)) with embedded Au nanoclusters. It is shown that the sensitivity of the developed SPR biosensor can be improved by adjusting the size and volume fraction of the embedded Au nanoclusters in order to control the surface plasmon effect. The present gas detection and DNA hybridization experimental results confirm that the proposed Au nanocluster-enhanced SPR biosensor provides the potential to achieve an ultrahigh-resolution detection performance of approximately 0.1 pg/mm(2) surface coverage of biomolecules.

Argon↗
PubMed2001

The intrinsic stability of the noble gas-coordinated transition-metal complex ions.

Density-functional-theory and high-level ab initio calculations have been performed on the [AuXe4]2+ ion and some other hypothetical xenon-, krypton-, and argon-coordinated transition-metal complex cations in the gas phase. Geometry optimization at the QCISD(T) level using a (6s7p4d2f1g) basis set for Au and a (4s4p2d1f) set for Xe predicted Au-Xe bond lengths in good agreement with the AuXe4(2+)(Sb2F11-)2 crystal structure. The ligand-binding energies of the [AuXe4]2+, [AuXe4]3+, and [PtXe4]2+ ions were predicted to be 229, 565, and 233 kcal/mol, respectively, at the CCSD(T) level. It is found that higher-level correlation effects are important to obtain accurate geometry parameters. The calculated results also indicated that various trivalent, tetravalent, and hexavalent transition-metal complexes of xenon or krypton might also be intrinsically stable.

Drug Stability↗
PubMed2000

Structure-function studies on Taiwan cobra long neurotoxin homolog.

A novel long neurotoxin homolog was purified from Naja naja atra (Taiwan cobra) venom using the combination of ion exchange chromatography and reverse phase high performance liquid chromatography. The determined protein sequence was essentially the same as that deduced from the cDNA amplified by reverse transcriptase-polymerase chain reaction. The long neurotoxin homolog exhibited an activity that inhibited acetylcholine-induced muscle contractions, as with N. naja atra cobrotoxin. The degree of inhibition caused by the addition of long neurotoxin homolog was approximately 70% of that observed with the addition of cobrotoxin. Unlike the well-known short and long neurotoxins, this neurotoxin homolog contained two additional cysteine residues forming a disulfide linkage in the N-terminal region. Circular dichroism measurement and computer models of the neurotoxin reveal that its secondary structure was not abundant in beta-sheet as noted with short and long neurotoxins. This less ordered structure may be associated with the lower activity noted with the long neurotoxin homolog. Together with the finding that the known long neurotoxin homologs exclusively appear in the venoms of the Naja and Bungarus genera, the long neurotoxin homologs should represent an evolutionary branch from the long and short neurotoxins in the Elapidae family.

Amino Acid Sequence↗
PubMed1998

DNA optical sensor: a rapid method for the detection of DNA hybridization.

A DNA optical sensor system is proposed based on the combination of sandwich solution hybridization, magnetic bead capture, flow injection and chemiluminescence for rapid detection of DNA hybridization. Bacterial alkaline phosphatase (phoA) gene and Hepatitis B virus (HBV) DNA were used as target DNA. A biotinylated DNA probe was used to capture the target gene onto the streptavidin-coated magnetic beads and a calf intestine alkaline phosphatase (CAP)-labelled DNA probe was used for subsequent enzymatic chemiluminescence detection. The detection cycle was less than 30 min, excluding the DNA hybridization time, which was about 100 min. Both the phoA gene and HBV DNA could be detected at picogramme or femtomole level. No response signal was obtained when target DNA did not exist in the sample. Successive sample detection could be made by removing the magnetic field and a washing step.

Biosensing Techniques↗
PubMed1997

Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns.

A new and more accurate method has been developed for predicting the backbone U-turn positions (where the chain reverses global direction) and the dominant secondary structure elements between U-turns in globular proteins. The current approach uses sequence-specific secondary structure propensities and multiple sequence information. The latter plays an important role in the enhanced success of this approach. Application to two sets (total 108) of small to medium-sized, single-domain proteins indicates that approximately 94% of the U-turn locations are correctly predicted within three residues, as are 88% of dominant secondary structure elements. These results are significantly better than our previous method (Kolinski et al., Proteins 27:290-308, 1997). The current study strongly suggests that the U-turn locations are primarily determined by local interactions. Furthermore, both global length constraints and local interactions contribute significantly to the determination of the secondary structure types between U-turns. Accurate U-turn predictions are crucial for accurate secondary structure predictions in the current method. Protein structure modeling, tertiary structure predictions, and possibly, fold recognition should benefit from the predicted structural data provided by this new method.

Amino Acid Sequence↗
PubMed1997

Sequence-structure specificity--how does an inverse folding approach work?

The inverse folding approach is a powerful tool in protein structure prediction when the native state of a sequence adopts one of the known protein folds. This is because some proteins show strong sequence-structure specificity in inverse folding experiments that allow gaps and insertions in the sequence-structure alignment. In those cases when structures similar to their native folds are included in the structure database, the z-scores (which measure the sequence-structure specificity) of these folds are well separated from those of other alternative structures. In this paper, we seek to understand the origin of this sequence-structure specificity and to identify how the specificity arises on passing from a short peptide chain to the entire protein sequence. To accomplish this objective, a simplified version of inverse folding, gapless inverse folding, is performed using sequence fragments of different sizes from 53 proteins. The results indicate that usually a significant portion of the entire protein sequence is necessary to show sequence-structure specificity, but there are regions in the sequence that begin to show this specificity at relatively short fragment size (15-20 residues). An island picture, in which the regions in the sequence that recognize their own native structure grow from some seed fragments, is observed as the fragment size increases. Usually, more similar structures to the native states are found in the top-scoring structural fragments in these high-specificity regions.

Amino Acid Sequence↗
PubMed1997

A method for the prediction of surface "U"-turns and transglobular connections in small proteins.

A simple method for predicting the location of surface loops/turns that change the overall direction of the chain that is, "U" turns, and assigning the dominant secondary structure of the intervening transglobular blocks in small, single-domain globular proteins has been developed. Since the emphasis of the method is on the prediction of the major topological elements that comprise the global structure of the protein rather than on a detailed local secondary structure description, this approach is complementary to standard secondary structure prediction schemes. Consequently, it may be useful in the early stages of tertiary structure prediction when establishment of the structural class and possible folding topologies is of interest. Application to a set of small proteins of known structure indicates a high level of accuracy. The prediction of the approximate location of the surface turns/loops that are responsible for the change in overall chain direction is correct in more than 95% of the cases. The accuracy for the dominant secondary structure assignment for the linear blocks between such surface turns/loops is in the range of 82%.

Algorithms↗
PubMed1997

Method for low resolution prediction of small protein tertiary structure.

A new method for the de novo prediction of protein structures at low resolution has been developed. Starting from a multiple sequence alignment, protein secondary structure is predicted, and only those topological elements with high reliability are selected. Then, the multiple sequence alignment and the secondary structure prediction are combined to predict side chain contacts. Such contact map prediction is carried out in two stages. First, an analysis of correlated mutations is carried out to identify pairs of topological elements of secondary structure which are in contact. Then, inverse folding is used to select compatible fragments in contact, thereby enriching the number and identity of predicted side chain contacts. The final outcome of the procedure is a set of noisy secondary and tertiary restraints. These are used as a restrained potential in a Monte Carlo simulation of simplified protein models driven by statistical potentials. Low energy structures are then searched for by using simulated annealing techniques. Implementation of the restraints is carried out so as to take into account of their low resolution. Using this procedure, it has been possible to predict de novo the structure of three very different protein topologies: an alpha/beta protein, the bovine pancreatic trypsin inhibitor (6pti), an alpha-helical protein, calbindin (3icb), and an all beta- protein, the SH3 domain of spectrin (1shg). In all cases, low resolution folds have been obtained with a root mean square deviation (RMSD) of 4.5-5.5 A with respect to the native structure. Some misfolded topologies appear in the simulations, but it is possible to select the native one on energetic grounds. Thus, it is demonstrated that the methodology is general for all protein motifs. Work is in progress in order to test the methodology on a larger set of protein structures.

Amino Acid Sequence↗