Biomedical subjects

V Renugopalakrishnan

Publications and source records attributed to V Renugopalakrishnan.

At least 19 recordsLinked to original sources

PubMed2006

Thermal denaturation of a recombinant mouse amelogenin: circular dichroism and differential scanning calorimetric studies.

Conformational analyses of a recombinant mouse tooth enamel amelogenin (rM179) were performed using circular dichroism (CD), fluorescence, differential scanning calorimetry, and sedimentation equilibrium studies. The results show that the far-UV CD spectra of rM179 at acidic pH and 10 degrees C are different from the spectra of random coil in 6 M GdnHCl. A near-UV CD spectrum of rM179 at 10 degrees C is similar to that of rM179 in 6 M GdnHCl, which indicates that aromatic residues of native structure are exposed to solvent and rotate freely. Far-UV CD values of rM179 at 80 degrees C are different from that of random-coil structure in 6 M GdnHCl, which suggests that rM179 at 80 degrees C has specific secondary structures. A gradual thermal transition was observed by far-UV CD, which is interpreted as a weak cooperative transition from specific secondary structures to other specific secondary structures. The fluorescence emission maximum for the spectrum due to Trp residues in rM179 at 10 degrees C shows the same fluorescence emission maximum as rM179 in 6 M GdnHCl and amino acid Trp, which indicates that the three Trp in rM179 are exposed to solvent. Deconvolution of differential scanning calorimetry curve gives the population of three states (A, I, and C states). These results indicate that three states (A, I, and C) have specific secondary structures, in which hydrophobic and Trp residues are exposed to the solvent. The thermodynamic characteristics of rM179 are unique and different from a typical globular protein, proline-rich peptides, and a molten globule state.

Amelogenin↗

PubMed2005

Electrostatics of Cytochrome-c assemblies.

Electrostatic potentials along with computational mutagenesis are used to obtain atomic level insights into Cytochrome-c in order to design efficient bionanosensors. The electrostatic properties of wild type and mutant Cytochrome-c are examined in the context of their assembly, i.e. are examined in the absence and presence of neighboring molecules from the assembly. An intense increase in the positive potential ensues when the neighboring molecules are taken into account. This suggests that in the extrapolation of electric field effects upon the design of assemblies, considering the properties of only the central molecule may not be sufficient. Additionally, the influence of the uncharged residues becomes quite diminished when the molecule is considered in an assembly. This could pave the way for making mutants that might be more soluble in different media used in the construction of devices. [Figure: see text]. The electrostatic potential, calculated using the program DELPHI mapped on to the surface of Cytochrome-c when it is considered by itself (in the left column) and in the presence of the electrostatic field generated by the presence of the surrounding 4 molecules on the right. The potentials range from -10kT in red to +10kT in blue. The central figure shows the regions that have been mutated to positively charged residues by placing a unit positive charge at the terminal atom of the respective side chain. The figures range from the wild type in the first row, followed by the Gln12, Asn70, Asp50, Glu90 and Ala83 mutants.

Cytochromes c↗

PubMed2005

Rational design of thermally stable proteins: relevance to bionanotechnology.

Design of thermally stable proteins is spurred by their applications in bionanotechnology. There are three major issues governing this: first, the upper limit on the temperature at which proteins remain physiologically active and are available for technological applications (answers may emerge from the discovery of new, natural hyperthermophilic enzymes that are active above 125 degrees C or from the selection of mutants of hyperthermophilic enzymes that are more stable); second, the use of hyperthermophilic enzymes as molecular templates to design highly stable enzymes that have high activity at low temperatures; third, the link between rigidity and flexibility to thermostability and activity, respectively. We review progress in these areas.

Bacteriorhodopsins↗

PubMed2003

Ultrastructure of dental enamel afflicted with hypoplasia: an atomic force microscopic study.

The ultrastructure of the human tooth enamel from a patient diagnosed with hypoplasia (HYP) was investigated using atomic force microscopy (AFM) and compared with the surface of normal human tooth enamel. Hypoplasia is a hereditary defect of dental enamel in which the enamel is deficient in either quality or quantity. AFM results presented for the HYP tooth enamel clearly demonstrate that the apatite crystal morphology in hypoplasia tooth enamel is perturbed in the diseased state which could result from a defective synthesis of the extracellular matrix proteins, e.g., amelogenin, by the ameloblasts. HYP enamel consisting of loosely packed, very small grains does not present a tendency for association, as in the case of the normal healthy tooth. Indeed, the enamel surface affected by HYP is porous and is made of much smaller grains. In some samples, the HYP part of enamel surface appeared in the form of a point-defect, which we believe may be associated with the early stages of the HYP deformation.

Apatites↗

PubMed2002

A 27-mer tandem repeat polypeptide in bovine amelogenin: synthesis and CD spectra.

CD spectra of a tandem 27-mer repeat polypeptide, Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-Met-(Gln-Pro-Leu)4, from bovine amelogenin synthesized by standard solid-phase synthesis manifests an archtypical CD pattern of a beta-spiral structure in phosphate buffer at pH 5.2 and trifluoroethanol (TFE), CF3OH. beta-spiral structure is unique to a class of diverse proteins including amelogenins conferring unusual physicochemical properties.

Amelogenin↗

PubMed2002

An atomic force microscopic study of the ultrastructure of dental enamel afflicted with amelogenesis imperfecta.

The ultrastructure of human tooth enamel from a patient diagnosed to have amelogenesis imperfecta (AI) was investigated using atomic force microscopy (AFM) and compared with normal human tooth enamel. AI is a hereditary defect of dental enamel in which the enamel is deficient in either quality or quantity. Tissue-specific proteins, especially amelogenins, have been postulated to play a central role in amelogenesis. The secondary structure of amelogenin has been assigned an important role in directing the architecture of hydroxyapatite (HA) enamel crystallites and an alteration of the secondary structure of amelogenin is expected to result in an altered architecture of the mineral phase in human enamel. Previous studies have shown that the human amelogenin gene encodes for a mutant protein in which a conserved Pro is mutated to a Thr residue (Pro-->Thr); such a mutation should be expected to cause a disoriented pattern of the mineral phase in enamel. AFM results presented for the AI tooth enamel clearly demonstrate that the apatite crystal morphology in AI tooth enamel is perturbed in the diseased state; this might result from a defective synthesis of the extracellular matrix proteins, e.g. amelogenin, by the ameloblasts.

Adult↗

PubMed2001

Glycosylated and phosphorylated proteins--expression in yeast and oocytes of Xenopus: prospects and challenges--relevance to expression of thermostable proteins.

Phosphorylation and glycosylation are important posttranslational events in the biosynthesis of proteins. The different degrees of phosphorylation and glycosylation of proteins have been an intriguing phenomenon. Advances in genetic engineering have made it possible to control the degree of glycosylation and phosphorylation of proteins. Structural biology of phosphorylated and glycosylated proteins has been advancing at a much slower pace due to difficulties in using high-resolution NMR studies in solution phase. Major difficulties have arisen from the inherent mobilities of phosphorylated and glycosylated side chains. This paper reviews molecular and structural biology of phosphorylated and glycosylated proteins expressed in eukaryotic expression systems which are especially suited for large-scale production of these proteins. In our laboratory, we have observed that eukaryotic expression systems are particularly suited for the expression of thermostable light-activated proteins, e.g., bacteriorhodopsins and plastocyanins.

Animals↗

PubMed1999

Human pancreatic thread protein, an exocrine thread protein with possible implications to Alzheimer's disease: secondary structure in solution at acid pH.

The secondary structure of human pancreatic thread protein (HPTP) in solution at acid pH was derived using Fourier transform infrared (FT-IR) and laser Raman spectroscopic studies. The experimentally derived secondary structure of HPTP was compared with the secondary structure obtained by the Chou-Fasman algorithm. Pancreatic thread protein is a major exocrine secretory protein that in vitro forms filamentous bundles reminiscent of the paired helical filaments of Alzheimer's disease (AD). PTP immunoreactivity in brains afflicted with AD has been demonstrated previously and high levels of its mRNA in the developing human brain have also been reported in the literature. The above studies suggest that AD is associated with enhanced expression of PTP-related transcripts with interneuronal accumulation of PTP-like proteins. The experimentally derived secondary structure of HPTP consists of a significant proportion of beta-sheets and beta-turns and lesser amounts of alpha-helical structures. The beta-sheet component presumably plays an important role in the pH-dependent globule-fibril transformation of HPTP leading to antiparallel beta-sheet structure in the aggregated state. The secondary structure of HPTP and its globule-fibril transformation lend credence to the belief that AD may be viewed as a conformational disease.

Algorithms↗

PubMed1999

Partitioning of Polymerizing Fluids in Random Microporous Media: Application of the Replica Ornstein-Zernike Equations.

We have investigated a model for a polymerizing fluid in which each of the particles has two bonding sites, such that chains can be formed via a chemical association mechanism. The fluid model is considered to be in a random quenched microporous matrix. The matrix species are assumed to be either impermeable to adsorbed fluid particles or permeable, such that the surface of the matrix particles represents a permeable membrane of finite width. We have studied the influence of the matrix species on the formation of chains due to association. The model is investigated by means of the associative replica Ornstein-Zernike equations with the Percus-Yevick closure and the ideal chain approximation. We have observed that the average chain length is longer in the presence of an impermeable matrix than in the case where the matrix is absent. Matrix is therefore conducive to the growth of the polymerizing species in micropores. There is a decrease in the average chain length with increasing permeability of matrix species. This behavior reaffirms the attenuating role of the permeable matrix species as a whole. Copyright 1999 Academic Press.

Journal Article↗

PubMed1998

Structural studies of cucumber mosaic virus: Fourier transform infrared spectroscopic studies.

The secondary structure of cucumber mosaic virus (CMV) was investigated in solution using Fourier transform infrared (FT-IR) spectroscopy. The amide I region of intact CMV revealed a doublet at 1671 cm-1 and 1653 cm-1, respectively. In order to isolate the IR bands arising from the protein backbone of CMV, the FT-IR spectra of the RNA component, isolated by phenol-SDS treatment of purified CMV and subsequent precipitation by ethanol, was obtained separately and digitally subtracted from the intact CMV spectra. After digital subtraction, the amide I region contained two bands at 1682 cm-1 and 1644 cm-1. The former band was ascribed to beta-sheet structures, while the later band occurs in the region between alpha-helix and "unordered" structures. Resolution enhancement of the finger print amide I region was accomplished using Fourier self-deconvolution of the digitally subtracted FT-IR spectrum of CMV which further confirmed the presence of anti-parallel beta-sheet structure in the protein coat of CMV. Chou-Fasman predictions on the the coat protein also revealed the presence of beta-sheet structure in agreement with FT-IR studies.

Capsid↗

PubMed1993

Estimation of the secondary structure and conformation of bovine lens crystallins by infrared spectroscopy: quantitative analysis and resolution by Fourier self-deconvolution and curve fit.

The secondary structure of six bovine lens protein fractions (two alpha, three beta and one gamma-crystallin) are examined in solution and in solid forms for the first time using FTIR spectroscopy. Films of the nuclear and cortical regions of the bovine lens are also examined. The structure is quantitatively estimated from the vibrational analysis of the resolution-enhanced amide-I profile achieved by Fourier self-deconvolution and linear least-squares curve-fit algorithm. All the protein fractions fold predominantly in a beta-pleated sheet structure with little or no alpha-helical domains in solution or in lyophilized solid form. These proteins also retain their predominant beta-sheet conformation in the cellular phospholipid environment of the lens, in conformity with the structure obtained for all the mammalian species examined to date. Despite structural homology, vibrational data indicate subtle structural differences within each class of the crystallins probably due to presence of several minor substructures/subconformations. Substantial high amounts of turns (approx. 40%) observed in the beta-fractions may have a fundamental implication in stabilizing the tertiary structure of the uniquely folded-proteins vital for the transparency of the lens. These proteins in solid KBr-matrix undergo a major structural change, induced primarily by ionic interactions which refold them in a helical conformation. IR spectroscopy together with band-narrowing procedures has proven to be an effective tool to obtain structural information of proteins in solution, as solid substrates or in a complex biological tissue, such as ocular lens.

Algorithms↗

PubMed1991

Fourier transform infrared spectroscopic study of the carbonate ions in bone mineral during aging.

The environment of CO3(2-) ions in the bone mineral of chickens of different ages and in bone fractions of different density have been investigated by resolution-enhanced Fourier Transform Infrared (FTIR) Spectroscopy. Three carbonate bands appear in the upsilon 2 CO3 domain at 878, 871, and 866 cm-1, which may be assigned to three different locations of the ion in the mineral: in monovalent anionic sites of the apatitic structure (878 cm-1), in trivalent anionic sites (871 cm-1), and in unstable location (866 cm-1) probably in perturbed regions of the crystals. The distribution of the carbonate ions among these locations was estimated by comparing the intensities of the corresponding FTIR spectral bands. The intensity ratio of the 878 and 871 cm-1 bands remains remarkably constant in whole bone as well as in the fractions obtained by density centrifugation. On the contrary, the intensity ratio of the 866 cm-1 to the 871 cm-1 band was found to vary directly and decreased with the age of the animal. In bone of the same age, the relative content of the unstable carbonate ion was found to be highest in the most abundant density centrifugation fraction. A resolution factor of the CO3(2-) band (CO3 RF) was calculated from the FTIR spectra which was shown to be very sensitive to the degree of crystallinity of the mineral. The crystallinity was found to improve rapidly with the age of the animal. The CO3 RF in the bone samples obtained by density centrifugation from bone of the same animal was found to be essentially constant.(ABSTRACT TRUNCATED AT 250 WORDS)

Aging↗

PubMed1991

A resolution-enhanced Fourier transform infrared spectroscopic study of the environment of the CO3(2-) ion in the mineral phase of enamel during its formation and maturation.

A resolution-enhanced Fourier Transform Infrared (FTIR) Spectroscopic study of the CO3(2-) ion in pig enamel of increasing age and maturity has demonstrated the existence of four different, main carbonate locations. The major CO3(2-) site arises as a result of the substitution of CO3(2-) ions in the positions occupied by PO4(3-) ions in the apatitic lattice. In addition, two minor locations have been identified in positions in which the CO3(2-) ions substitute for OH- ions. The fourth carbonate group appears to be in an unstable location. Its concentration has been found to decrease with aging and maturation, during which there is a progressive increase in the amount of mineral deposited in the enamel. The distribution of the carbonate ions in the different apatitic sites varies randomly during the formation of the mineral phase in enamel and during its maturation. Although these changes have been shown to be related to changes in the composition of the mineral phase, a comparison of the parameters assessing the degree of crystallinity of the mineral phase from upsilon 2CO3(2-) and upsilon 4PO4(3-) infrared absorption data reveals a significant discrepancy related to the nonhomogeneous partition of the CO3(2-) ion in the mineral phase. After maximum mineralization is reached, the composition of the mature mineral phase is decidedly different than that of the initial mineral deposited; the changes affect principally the concentrations of Ca2+, OH-, and HPO4(2-) ions, but not the CO3(2-) ions.

Aging↗

PubMed1990

Conformational transitions in phosvitin with pH variation. Vibrational circular dichroism study.

The vibrational circular dichroism (VCD) spectra of metal-free phosvitin are presented as a function of pH and analyzed both qualitatively and by using a factor analysis approach referenced to a protein data set. The qualitative pattern of both the IR and VCD changes is consistent with a coil-to-sheet transition occurring as pH is progressively decreased to values lower than 3. A similar transition was seen in commercial preparation of phosvitin which still contained metal ions, but there the transition was more gradual and occurred at somewhat different pH values. Such a gradual change is also evident in the solution phase absorption band profile but is made clearer using Fourier deconvolution. Based on VCD results, the low pH transition appears to occur with two distinct manifestations of the beta-sheet form. However, at the lowest pH values the sample may precipitate. These two forms are not distinguishable with Fourier transform infrared alone and may be due to a twist of the beta-sheet form or to aggregation.

Circular Dichroism↗

PubMed1989

Synthesis and biological properties of 4-norleucine-neuropeptide Y; secondary structure of neuropeptide Y.

Neuropeptide Y (NPY) is a 36 amino acid peptide amide isolated from porcine brain. The NPY analog, 4-norleucine-NPY was synthesized by a solid-phase method and purified to homogeneity in 20% yield by reverse-phase chromatography. Investigation of the biological properties indicated that the analog is an agonist of NPY. Secondary structural analyses revealed that NPY and the analog exhibited predominantly alpha-helical and beta-sheet structures, respectively; however, experiments in trifluoroethanol indicated that the analog has the potential of assuming an alpha-helical structure. Based on circular dichroism (CD), Raman spectroscopy and Chou-Fasman analyses, a model has been proposed for the secondary structure of NPY.

Amino Acid Sequence↗

PubMed1989

Tooth enamel protein, amelogenin, has a probable beta-spiral internal channel, Gln112-Leu138, within a single polypeptide chain: preliminary molecular mechanics and dynamics studies.

Molecular dynamics simulation, with backbone constraints for 20 ps of equilibration and simulation, of a repeating polypeptide segment, Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-Met-(Gln-Pro-Leu )4, constituting residues 112-138 of bovine amelolgenin, a 19.35 kD hydrophobic protein, are discussed. It is generally believed that the above polypeptide segment is important for the interaction of amelogenin with Ca++ ions, which occurs in the early phases of enamel mineralization. An energetically stable structure of the above polypeptide with recurrent beta-turns is observed and contains a pore of approximately 1 A radius along the helical that can accommodate an unhydrated Ca++ ion. The length of the polypeptide possesses correct dimensions to span a bilayer. The proposed structure is unique among known polypeptide and protein structures.

Amelogenin↗

PubMed1989

Secondary structure of a core protein from pig skin proteodermatan sulfate: CD and Fourier transform IR spectroscopic studies in solution.

The secondary structure of a 38 kDa core protein from pig skin proteodermatan sulfate (PDS), was investigated in solution using CD and Fourier transform (FT) ir spectroscopy. Both techniques generally have provided complementary data on the secondary structures of proteins. CD spectral analysis has shown that the core protein contains 60% beta-turn and alpha-helical structures, the rest being "unordered" structure. FT ir data do not permit calculation of quantitative contributions of substructures, at the present time, to the overall secondary structure of the core protein. CD spectrum of the intact PDS is similar to the core protein CD spectrum.

Animals↗

PubMed1989

Secondary structure of pig skin proteodermatan sulfate: a perspective from Raman spectroscopic studies in aqueous solution.

Raman spectroscopic studies of pig skin proteodermatan sulfate in H2O are indicative of a well defined secondary structure consisting of alpha-helical, beta-turn, and possibly "random" structures. The above conclusion is surprisingly close to the secondary structure of the "core" protein of pig skin proteodermatan sulfate proposed in the previous paper (V. Renugopalakrishnan et al., Biopolymers 28, 1923-1933, 1989) from FT-IR and CD spectroscopic studies in aqueous solution.

Animals↗