Biotech boom

India's thriving biotechnology industry is threatened by a change in the law. Will the current high levels of investment be enough to secure its future?     

Common binding site for disialyllactose and tri-peptide in C-fragment of tetanus neurotoxin

Clostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. Crystal structures of the binding domain of TeNT complexed with disialyllactose (DiSia) and a tri-peptide Tyr-Glu-Trp (YEW) have been determined to 2.3 and 2.2 A, respectively. Both DiSia and YEW bind in a shallow cleft region on the surface of the molecule in the beta-trefoil domain, interacting with a set of common residues, Asp1147, Asp1214, Asn1216, and Arg1226. DiSia and YEW binding at the same site in tetanus toxin provides a putative site that could be occupied either by a ganglioside moiety or a peptide. Soaking experiments with a mixture of YEW and DiSia show that YEW competes with DiSia, suggesting that YEW can be used to block ganglioside binding. A comparison with the TeNT binding domain in complex with small molecules, BoNT/A and /B, provides insight into the different modes of ganglioside binding.     

Immunodepletion of albumin for two-dimensional gel detection of new mouse acute-phase protein and other plasma proteins

Immunodepletion of albumin to improve the 2-D gel resolution of human plasma proteins has recently been described. With the importance of mouse models in many studies in which serum or plasma is often analyzed, we have adopted this approach to immunoprecipitate mouse albumin and evaluated its effectiveness for 2-D separation of mouse plasma proteins. Purified polyclonal antibodies against mouse albumin were effective depleting intact albumin as well as its numerous fragments from mouse plasma samples. Removal of albumin resulted in better resolution of mouse plasma proteins. Three proteins, alpha2-macroglobulin, coagulation factor XII, and hemopexin, that were previously either undetectable or poorly resolved, were identified from albumin-depleted 2-D gels by peptide mass fingerprinting. Albumin depletion also led to partial loss of several other proteins such as clusterin and gelsolin. This loss can be attributed to the interaction with albumin itself because the specificity of the antibody was demonstrated by Western blot. When applying this method to the 2-D separation of plasma from inflamed mouse induced by cutaneous burn injury with superimposed Pseudomonas aeruginosa infection, the upregulation of inter alpha-trypsin inhibitor heavy chain 4 (ITIH4) and hemopexin was unambiguously detected along with other mouse acute-phase proteins (APP), including haptoglobin and serum amyloid A. Based on the significant increase of ITIH4, we propose that this protein is a new member of mouse APP that are upregulated during the inflammatory response.     

Enhanced catalytic and conformational stability of Atlantic cod trypsin upon neoglycosylation

The applicability of psychrophilic enzymes is limited because of their lower thermodynamic stability in spite of their higher catalytic rate. In this study, we have shown that the thermodynamic stability of the psychrophilic Atlantic cod trypsin could be enhanced appreciably by covalent chemical modification with oxidized sucrose polymer without affecting its hydrolytic activity. The acquired stability of cod trypsin was found to be on par with the mesophilic porcine trypsin.     

Structural basis for thermal stability of human low-density lipoprotein

The stability of human low-density lipoprotein (LDL), the major cholesterol carrier in plasma, was analyzed by heating samples of different concentrations at a rate from 11 to 90 K/h. Correlation of the calorimetric, circular dichroism, fluorescence, turbidity, and electron microscopic data shows that thermal disruption of LDL involves irreversible changes in the particle morphology and protein conformation but no global protein unfolding. Heating to 85 degrees C induces LDL conversion into smaller and larger particles and apparent partial dissociation, but not unfolding, of its sole protein, apoB. Further heating leads to partial unfolding of the beta-sheets in apoB and to fusion of the protein-depleted LDL into large aggregated lipid droplets, resulting in a previously unidentified high-temperature calorimetric peak. These lipid droplets resemble in size and morphology the extracellular lipid deposits formed in the arterial wall in early atherosclerosis. The strong concentration dependence of LDL fusion revealed by near-UV/visible CD, turbidity, and calorimetry indicates high reaction order, and the heating rate dependence suggests high activation energy that arises from transient disruption of lipid and/or protein packing interactions in the course of particle fusion and apparent apoB dissociation. Consequently, thermal stability of LDL is modulated by kinetic barriers. Similar barriers may confer structural integrity to LDL subclasses in vivo.     

A rapid algorithm for processing digital physiologic signals: Application to skeletal muscle contractions

Quantifying mechanical output is fundamental to understanding metabolism that fuels muscle contraction and more recent attempts to understand signal transduction and gene regulation. The latter requires long-term application of exercise protocols that result in large amounts of data on muscle performance. The purpose of this study was to develop software for automated quantification of skeletal muscle contractions. An in situ mouse sciatic nerve stimulation model was used to produce contractions over a broad range of frequencies and recorded as both digital and analog signals using a PC analog to digital converter board and chart recorder, respectively. Spectral analysis of the noise components formed the basis for designing a smoothing Chebyshev filter. Algorithms implemented in custom software identified twitches and estimated baseline levels from the smoothed signal. The time to peak force, peak force, tension-time integral, and half-relaxation time were determined for each twitch after baseline correction. The automated results were compared to those obtained from manual measurements of the analog signal. Bland–Altman analysis of the parameters computed from digital signals compared with the corresponding measurements by manual planometry demonstrates the agreement of the digital processing algorithm with planometry over a wide range of twitch characteristics. This program may also be used to study the mechanics of other preparations from isolated muscles, human proximal limb performance, and other digital physiologic signals. Adaptation of the filter function is required to apply the analysis to another experimental apparatus with differing noise characteristics. A full version of the program and instructions for its use are available for download at www.rad.msu.edu.     

Computer simulation study of molecular recognition in model DNA microarrays

DNA microarrays have been widely adopted by the scientific community for a variety of applications. To improve the performance of microarrays there is a need for a fundamental understanding of the interplay between the various factors that affect microarray sensitivity and specificity. We use lattice Monte Carlo simulations to study the thermodynamics and kinetics of hybridization of single-stranded target genes in solution with complementary probe DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8-24 segments. The segments on the probe and target are distinct and each segment represents a sequence of nucleotides ( approximately 11 nucleotides). Each probe segment interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how the probe length, temperature, or hybridization energy, and the stretch along the target that the probe segments complement, affect the extent of hybridization. For systems containing single probe and single target molecules, we observe that as the probe length increases, the probability of binding all probe segments to the target decreases, implying that the specificity decreases. We observe that probes 12-16 segments ( approximately 132-176 nucleotides) long gave the highest specificity and sensitivity. This agrees with the experimental results obtained by another research group, who found an optimal probe length of 150 nucleotides. As the hybridization energy increases, the longer probes are able to bind all their segments to the target, thus improving their specificity. The hybridization kinetics reveals that the segments at the ends of the probe are most likely to start the hybridization. The segments toward the center of the probe remain bound to the target for a longer time than the segments at the ends of the probe.     

Conformational space exploration of Met- and Leu-enkephalin using the MOLS method, molecular dynamics, and Monte Carlo simulation--a comparative study

We report here a comparative study of the molecular conformational energy landscape generated using the mutually orthogonal Latin squares (MOLS) method, molecular dynamics (MD), and Monte Carlo (MC) simulation. The MOLS method, as described earlier from our laboratory, uses an experimental design technique to rapidly and exhaustively sample the low energy conformations of a molecule. MD and MC simulations have been used to perform similar tasks. In the comparison reported here, the three methods were applied to a pair of neuropeptides, namely Met- and Leu-enkephalin. A set of 1500 conformations of these enkephalins were generated using these methods with CHARMM22 force field, and the resulting samples were analyzed to determine the extent and nature of coverage of the conformational space. The results indicate that the MOLS method samples a larger number of possible conformations and identifies conformations closer to the experimental structures than the MD and MC simulations.     

Transforming growth factor-β inhibits cystogenesis in human autosomal dominant polycystic kidney epithelial cells

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited cause of kidney failure and characterized by the formation of multiple fluid-filled cysts in the kidneys. It is believed that environmental factors may play an important role in the disease progression. However, the molecular identity of autocrine/paracrine factors influencing cyst formation is largely unknown. In this study, we identified transforming growth factor-β2 (TGF-β2) secreted by normal human kidney (NHK) and ADPKD cells as an inhibitor of cystogenesis in 3D culture system using ADPKD cells from human kidneys. TGF-β2 was identified in conditioned media (CM) of NHK and ADPKD cells as a latent factor activated by heat in vitro. While all TGF-β isoforms recombinant proteins (TGF-β1, -β2, or -β3) displayed a similar inhibitory effect on cyst formation, TGF-β2 was the predominant isoform detected in CM. The involvement of TGF-β2 in the suppression of cyst formation was demonstrated by using a TGF-β2 specific blocking antibody and a TGF-β receptor I kinase inhibitor. TGF-β2 inhibited cyst formation by a mechanism other than activation of p38 mitogen-activated protein (MAP) kinase that mediated cell death in ADPKD cells. Further, we found that TGF-β2 modulated expression of various genes involved in cell-cell and cell-matrix interactions and extracellular matrix proteins that may play a role in the regulation of cystogenesis. Collectively, our results suggest that TGF-β2 secreted by renal epithelial cells may be an inhibitor of cystogenesis influencing the progression of ADPKD.