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L Ramdas

Publications and source records attributed to L Ramdas.

At least 19 recordsLinked to original sources
PubMed2001

Sources of nonlinearity in cDNA microarray expression measurements.

BACKGROUND: A key assumption in the analysis of microarray data is that the quantified signal intensities are linearly related to the expression levels of the corresponding genes. To test this assumption, we experimentally examined the relationship between signal and expression for the two types of microarrays we most commonly encounter: radioactively labeled cDNAs on nylon membranes and fluorescently labeled cDNAs on glass slides. RESULTS: We uncovered two sources of nonlinearity. The first, which led to discrepancies in analysis affecting the fluorescent signals, was signal quenching associated with excessive dye concentrations. The second, affecting the radioactive signals, was a nonlinear transformation of the raw data introduced by the scanner. Correction for this transformation was made by some, but not all, image-quantification software packages. CONCLUSIONS: The second type of nonlinearity is more troublesome, because it could not have been predicted a priori. Both types of nonlinearities were detected by simple dilution series, which we recommend as a quality-control step.

Calibration↗
PubMed2001

Sequence verification as quality-control step for production of cDNA microarrays.

To generate cDNA arrays in our core laboratory, we amplified about 2300 PCR products from a human, sequence-verified cDNA clone library. As a quality-control step, we sequenced the PCR products immediately before printing. The sequence information was used to search the GenBank database to confirm the identities. Although these clones were previously sequence verified by the company, we found that only 79% of the clones matched the original database after handling. Our experience strongly indicates the necessity to sequence verify the clones at the final stage before printing on microarray slides and to modify the gene list accordingly.

Gene Library↗
PubMed2001

Comparative evaluation of laser-based microarray scanners.

Laboratories use different laser-based scanners to scan microarray images. To assess whether results from different scanners are comparable, and thus whether data from different laboratories can be compared, we scanned the same microarray slide with three commercial scanners that use different imaging techniques. After the acquisition of the microarray images produced by the three scanners, the images were quantified using a single imaging software package and protocol. The results were compared, and we found that the data obtained from the three scanners were comparable and that the variations caused by the use of different instruments were negligible, in spite of the fact that the scanners were based on different optical imaging techniques.

Carbocyanines↗
PubMed2000

Cyclic peptides incorporating 4-carboxyphenylalanine and phosphotyrosine are potent inhibitors of pp60(c-)(src).

The protein tyrosine kinase, pp60(c-)(src), is involved in cellular signaling and is activated during mitosis and in various tumors. We have been employing cyclic decapeptides to identify the determinants for substrate binding and phosphorylation to develop inhibitors competitive with protein substrates of Src. A structure-activity study [McMurray, J. S., Budde, R. J. A., Ke, S., Obeyesekere, O. U., Wang, W., Ramdas, L., and Lewis, C. A. (1998) Arch. Biochem. Biophys. 355, 124] revealed that, at the position 3 residues C-terminal to the phosphorylated tyrosine (Y + 3), both glutamic acid and phenylalanine gave identical K(i), K(m), and V(max) values. We hypothesized that the area of Src that binds the Y + 3 residue contains either a positively charged lysine or an arginine, capable of ionic interactions with glutamic acid or cation-pi interactions with phenylalanine. To test this hypothesis, a series of phenylalanine analogues were substituted at position 7 (the Y + 3 residue) in cyclo(Asp(1)-Asn(2)-Glu(3)-Tyr(4)-Ala(5)-Phe(6)-Phe(7)-Gln(8)-D-Phe(9 )-Pro(10)). Of these, 4-carboxyphenylalanine (4-Cpa) and phosphotyrosine resulted in high affinity peptides exhibiting K(i) values of 0.85 and 1.1 microM, respectively, 180- and 130-fold increases in potency over the parent cyclic peptide (K(i) = 150 microM). These peptides were noncompetitive with respect to ATP and competitive against the phosphate-accepting substrate, polyGlu(4)Tyr. The truncated cyclic peptide, cyclo(Phe-4-Cpa-Gln-D-Phe-Pro-Asp-Aca) (Aca = epsilon-aminocaproic acid), which did not contain tyrosine, was also a competitive inhibitor with a K(i) value of 24 microM. We conclude that these cyclic peptides bind to a positively charged area that is near the phosphate transfer region of the active site of Src but does not necessarily include the tyrosine-binding pocket. Furthermore, the 4-Cpa-containing cyclic decapeptide shows remarkable selectivity in the inhibition of Src versus the src family members Yes and Lck, as well as other protein tyrosine kinases, Ser/Thr kinases, and other ATP-utilizing enzymes.

Animals↗
PubMed1999

Benzodiazepine compounds as inhibitors of the src protein tyrosine kinase: screening of a combinatorial library of 1,4-benzodiazepines.

We screened 1680 spatially separated compounds of a diverse combinatorial library of 1,4-benzodiazepines for their ability to inhibit the kinase activity of protein tyrosine kinases Src, Yes, Abl, Lck, Csk, and fibroblast growth factor receptor. This screening yielded novel ligands for the protein tyrosine kinase Src. In the 1, 4-benzodiazepine-2-one scaffold, the preferred substituent at position R(1) was 4-hydroxyphenylmethyl or a 3-indolemethyl derived from a tyrosine or tyrptophan used in building the benzodiazepine, while the substituent at R(2), introduced by alkylating agents, was preferably aromatic in nature. The preferred ring structure introduced on the bicyclic ring of the scaffold by acid chlorides was a p-hydroxy phenyl group. The lead compound, designated as N-L-Yaa, has a L-4-hydroxyphenylmethyl ring at R(1) and a biphenylmethyl substituent at R(2). The compound has an IC(50) of 73 microM against Src, 2- to 6-fold lower than against other protein tyrosine kinases and >10-fold lower than against other nucleotide-utilizing enzymes. The mechanism of binding of N-L-Yaa to Src is mixed against the peptidic substrate with a K(i) of 35 microM and noncompetitive against ATP-Mg with a K(i) of 17 microM. Multiple inhibition analysis of the lead compound in the presence of other competitive inhibitors demonstrated that the binding of the lead compound is nonexclusive to the other competitive inhibitor. The inhibitor was found to be nontoxic to the AFB-13-human fibroblasts cells and inhibited the colony formation of HT-29 colon adenocarcinoma cells that are dependent on Src activity.

Benzodiazepines↗
PubMed1999

N-myristoylation of a peptide substrate for Src converts it into an apparent slow-binding bisubstrate-type inhibitor.

The conversion of a peptide substrate to a potent inhibitor by chemical modification is a promising approach in the development of inhibitors for protein tyrosine kinases. N-acylation of the synthetic peptide substrate NH2-Glu-Phe-Leu-Tyr-Gly-Val-Phe-Asp-CONH2 (EFLYGVFD) resulted in synergistic inhibition of Src protein kinase activity that was greater than the inhibition by either free peptide and/or free acyl group. Synergistic inhibition was dependent upon the peptide sequence and the length of the acyl chain. The minimum length of the fatty acyl chain to synergistically inhibit Src was a lauryl (C11H23CO) group. N-myristoylated EFLYGVFD (myr-EFLYGVFD) inhibited the phosphorylation of poly E4Y by Src with an apparent Ki of 3 microm, whereas EFLYGVFD and myristic acid inhibited with Ki values of 260 and 35 microm, respectively. The nonacylated EFLYGVFD was a substrate for Src with Km and Vmax values of 100 microm and 400 nmol/min/mg protein, respectively. However, upon myristoylation, the peptide was no longer a substrate for Src. Both the acylated and non-acylated peptides were competitive inhibitors against the substrate poly E4Y. The non-acylated free peptide showed mixed inhibition against ATP while the myristoylated peptide was competitive against ATP. Myristic acid was uncompetitive against poly E4Y and competitive against ATP. Further analysis indicated that the myristoylated peptide acted as a reversible slow-binding inhibitor with two binding sites on Src. The myristoylated 8-mer peptide was reduced in size to a myristoylated 3-mer without losing the affinity or characteristics of a bisubstrate-type inhibitor. The conversion of a classical reversible inhibitor to a reversible slow-binding multisubstrate analogue has improved the potency of inhibition by the peptide.

Acylation↗
PubMed1998

Cyclic peptides as probes of the substrate binding site of the cytosolic tyrosine kinase, pp60c-src.

A series of 48 cyclic peptides based on the amino acid sequence surrounding the autophosphorylation site of pp60(c-src) was synthesized and each was tested as both a substrate and an inhibitor of this protein tyrosine kinase. Starting with cyclo(Asp1-Asn2-Gln3-Tyr4-Ala5-Ala6-Arg7-Gln8-d- Phe9-Pro10) a six-amino-acid survey was performed at positions 1 through 8 to determine which positions were critical for affinity and phosphorylation and which amino acids produced the greatest activity. Our survey found that Arg7 was detrimental for binding and phosphorylation and that aromatic residues were preferred at this position. Further increases in affinity were obtained with hydrophobic residues at position 6 with the optimum for both affinity and phosphorylation being Phe. Changes on the "amino-terminal" side of Tyr4 resulted in reduced Vmax values, illustrating the requirement for acidic residues in peptidic tyrosine kinase substrates. The result of the survey was cyclo(Asp1-Asn2-Gln3-Tyr4-Ala5-Phe6-Phe7-Gln8-d-Phe 9-Pro10). The change of residues 6 and 7 resulted in a 42-fold increase in affinity and no increase in Vmax. As a substrate, this peptide displayed Michaelis-Menten kinetics at saturating ATP conditions. As an inhibitor, mixed inhibition was observed. A linear version of this peptide was 13-fold less potent an inhibitor than the cyclic peptide.

Amino Acid Sequence↗
PubMed1998

The instability of polyhydroxylated aromatic protein tyrosine kinase inhibitors in the presence of manganese.

Inhibition of the tyrosine kinase activity of Src by forty-three different compounds from five chemical families (cinnamic acid, salicylic acid, phenol, coumarin and flavonoid derivatives) representing plant and microbial secondary metabolites were studied in the presence of MgCl2 versus MnCl2. Within each chemical family, compounds containing multiple hydroxyl substituents demonstrated the greatest inhibitor potency. The ortho-substituted dihydroxy compounds were the most inhibitory. Except for the flavonoids, inhibition was higher in the presence of manganese compared to that observed with magnesium. UV-Vis spectra, HPLC, and mass spectrometric analyses demonstrate that manganese catalyzed the oxidation of these compounds. The general instability of such compounds, especially in the presence of manganese, and the associated problems it causes in the use of such compounds for developing selective protein tyrosine kinase inhibitors, is discussed.

Animals↗
PubMed1996

A synthetic peptidic substrate of minimal size and semioptimal sequence for the protein tyrosine kinase pp60c-src.

We used a novel approach to determine the minimal size and semioptimal sequence of a peptide to serve as an inhibitor and/or substrate for the protein tyrosine kinase pp60c-src. The preferred amino acids surrounding tyrosine were determined by a systematic study in which we increased the length of a series of linear peptides starting from the tripeptide EYG. Using an iterative cycle, the size of the peptide was increased one residue at a time, first at the amino terminus and then at the carboxy terminus. A series of six analogs were synthesized at each position and assayed as inhibitors and substrates. The amino acids G, A, L, F, E, and K were used to semioptimize each position. The tripeptide EYG was not a substrate nor an efficient inhibitor. With increasing size of the peptide, the Ki decreased from 10.0 to 0.10 mM. The smallest peptide to serve as a substrate was a hexapeptide. The best overall peptide obtained from this method, EFEYAFF, had a Ki value of 0.13 mM with Km and Vmax values of 0.21 mM and 680 nmol/min/mg, respectively. Our best peptide was found to have higher substrate specificity than all other commerically available peptidic substrates for pp60c-src.

Amino Acid Sequence↗
PubMed1995

A tyrphostin-derived inhibitor of protein tyrosine kinases: isolation and characterization.

We recently reported that tyrphostin 23 (3,4-dihydroxybenzylidene malononitrile) is unstable in solution and that some of the degradation products are better inhibitors of the tyrosine kinase activity of Src and the EGF-receptor kinase than the parent compound itself (Ramdas et al., Cancer Res. 54, 867-868, 1994). In this study, the tyrphostin 23-derived compound designated P3, which is a more stable and potent protein tyrosine kinase inhibitor, was isolated. P3 was purified from oxidized tyrphostin 23 by solvent extraction, silica-gel flash chromatography, and reverse-phase high-pressure liquid chromatography. The physical characteristics of the isolated compound were determined and its chemical structure elucidated by 1H and 13C NMR spectroscopy. The proposed structure of this new inhibitor is that of a tyrphostin 23 dimer joined at the benzylidene carbon. P3 was evaluated in vitro as an inhibitor of four different protein tyrosine kinases (Src, Csk, EGF-receptor, and FGF-receptor) and two protein serine kinases (PK-A and PK-C). This compound exhibited the most inhibitory activity against Src with a Ki value of 6 microM and was less inhibitory toward the other protein kinases with Ki values ranging from 35 to 300 microM. P3 did not inhibit other nucleotide-utilizing enzymes such as lactate dehydrogenase and hexokinase. The growth and colony formation of HT-29 colon adenocarcinoma cells that contain activated Src was inhibited by P3 with an IC50 value of approximately 10 microM.

Catechols↗
PubMed1994

The degree of inhibition of protein tyrosine kinase activity by tyrphostin 23 and 25 is related to their instability.

Tyrphostins, a series of compounds with hydroxy cis-cinnamonitrile backbone structures, are used as protein tyrosine kinase inhibitors to study signal transduction. While studying the inhibition of pp60c-src protein tyrosine kinase activity with tyrphostins 23 and 25 (3,4-di- and 3,4,5-trihydroxy cis-cinnamonitrile), we found the inhibitors to be quite unstable. The inhibition of pp60c-src activity corresponded to the formation of products derived from the parent tyrphostin compound. One of these isolated products was at least 10-fold more inhibitory to both pp60c-src and epidermal growth factor receptor kinase activity than the parent tyrphostin. The generation of compounds more inhibitory than the parent tyrphostin may explain the delayed inhibition reported with epidermal growth factor receptor kinase activity. Since these tyrphostins are unstable and form compounds more inhibitory towards protein tyrosine kinase activity, any results obtained with these compounds must be interpreted with caution.

Catechols↗
PubMed1993

Recombinant pp60c-src from baculovirus-infected insect cells: purification and characterization.

A simple and effective method has been developed to purify the recombinant protein tyrosine kinase pp60c-src from a baculovirus-insect cell expression system. The procedure includes affinity chromatography and HPLC. Milligram quantities of protein have been isolated with an activity of 3.9 mumol/min/mg protein using the substrate poly E4Y. This specific activity is many times higher than any published protocol. The enzyme is stable for months when stored in buffered 10% glycerol at -70 degrees C. This purification technique is compared to the immuno-affinity technique which is widely used for this enzyme. Enzyme kinetics were characterized with respect to substrate specificity, the effect of temperature, ionic strength, pH, and Mg+2 versus Mn+2 ions. Similar to the enzyme expressed in human cells, the recombinant enzyme demonstrated a higher Vmax and substrate specificity for poly E4Y over 5V-Agt-II. An activation energy of 14.2 kcal/mol was determined. Inhibition by increasing ionic strength is mostly due to an increase in Km for the poly E4Y substrate and hence was substrate dependent. The Km(ATP) was pH dependent while the Km(poly E4Y) was pH independent. For the phosphorylation of poly E4Y, free Mg+2 was stimulatory while Mn+2 was inhibitory. In contrast, Mn+2 stimulated the phosphorylation of 5V-Agt-II.

Animals↗
PubMed1991

Nucleotide exchange and cGMP phosphodiesterase activation by pertussis toxin inactivated transducin.

Transducin, the signal coupling protein of retinal rod photoreceptor cells, is one of a family of G proteins that can be inactivated by pertussis toxin. We have investigated the nature of this inactivation in order to determine (1) whether it requires the toxin-catalyzed transfer of ADP-ribose from NAD+ to cysteine-347 of the alpha subunit and (2) whether it involves locking the alpha subunit in the inactive conformation characteristic of its GDP-bound state, or is limited to disruption of binding to photoexcited rhodopsin (R*). Our results indicate that all observed effects of pertussis toxin treatment, including a shift in the electrophoretic mobility of transducin's alpha subunit and functional inactivation, require NAD+ and that the appearance of the shift parallels incorporation of ADP-ribose. We have also found that, apart from interactions with photoexcited rhodopsin, the functional properties of ADP-ribosylated transducin are essentially the same as those of unmodified transducin. Normal spontaneous nucleotide exchange kinetics and the ability to activate cGMP phosphodiesterase are preserved following quantitative ADP-ribosylation, as are the abilities to hydrolyze GTP, to bind to a dye affinity column, and to display enhanced fluorescence upon addition of Al3+ and F-. Thus, ADP-ribosylation merely blocks catalysis of transducin nucleotide exchange by R* and does not lock transducin in an inactive state.(ABSTRACT TRUNCATED AT 250 WORDS)

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed1991

Amino acid sequence of rabbit apolipoprotein E.

The complete amino acid sequence of rabbit apolipoprotein E (apoE) was determined by generating three sets of peptides using cyanogen bromide, endoproteinase AspN, and Staphylococcus aureus V8 protease to cleave the protein. Through twenty cycles of sequence analysis on the whole protein, glutamic acid was identified as the N-terminal residue of rabbit apoE; the C-terminus of the protein was identified as glutamine. Based on the sequence of 294 amino acid residues determined by protein structure analysis, the molecular weight of rabbit apoE was determined to be 33,684. The protein sequence differed from the cDNA inferred sequence in 19 positions, only one of which could be attributed to microheterogeneity. The corrected amino acid sequence of rabbit apoE shares 80% homology with the human apoE sequence, 4% greater homology than that inferred from the cDNA sequence. The great similarity in the amino acid sequences of human and rabbit apoE suggests that their physical and physiological properties may also be similar. This homology and the relative ease with which apoE is isolated from rabbit plasma make it possible to conduct some in vitro experiments with the rabbit apoprotein that would have direct relevance to human apoE, but would be difficult or impossible with the human counterpart because of the quantity of protein required.

Amino Acid Sequence↗
PubMed1989

Replacement of a conserved proline and the alkaline conformational change in iso-2-cytochrome c.

Although point mutations usually lead to minor localized changes in protein structure, replacement of conserved Pro-76 with Gly in iso-2-cytochrome c induces a major conformational change. The change in structure results from mutation-induced depression of the pK for transition to an alkaline conformation with altered heme ligation. To assess the importance of position 76 in stabilizing the native versus the alkaline structure, the equilibrium and kinetic properties of the pH-induced conformational change have been compared for normal and mutant iso-2-cytochrome c. The pKapp for the conformational change is reduced from 8.45 (normal iso-2) to 6.71 in the mutant protein (Gly-76 iso-2), suggesting that conservation of Pro-76 may be required to stabilize the native conformation at physiological pH. The kinetics of the conformational change for both the normal and mutant proteins are well-described by a single kinetic phase throughout most of the pH-induced transition zone. Over this pH range, a minimal mechanism proposed for horse cytochrome c [Davis, L. A., Schejter, A., & Hess, G. P. (1974) J. Biol. Chem. 249, 2624-2632] is consistent with the data for normal and mutant yeast iso-2-cytochromes c: NH KH----N + H+ kcf in equilibrium kcb A NH and N are native forms of cytochrome c with a 695-nm absorbance band, A is an alkaline form that lacks the 695-nm band, KH is a proton dissociation constant, and kcf and kcb are microscopic rate constants for the conformational change. The Gly-76 mutation increases kcf by almost 70-fold, but kcb and KH are unchanged.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytochrome c Group↗
PubMed1988

Construction and characterization of mutant iso-2-cytochromes c with replacement of conserved prolines.

Oligonucleotide-directed mutagenesis has been used to construct two mutant forms of iso-2-cytochrome c. In one, Pro-30 is replaced by threonine; in the other, Pro-76 is replaced by glycine. Both prolines are fully conserved among mitochondrial cytochromes c and play important structural and functional roles. Yeast with either the Pro-30 or the Gly-76 mutation has appreciable levels of mutant protein in vivo and grows on media containing nonfermentable carbon sources. Thus, neither mutation blocks protein targeting to mitochondria, uptake by mitochondria, covalent attachment of heme, or in vivo function. As judged by ultraviolet-visible spectrophotometry and proton nuclear magnetic resonance spectroscopy, the nativelike conformation of purified Gly-76 iso-2 at pH 6 is almost indistinguishable from that of the normal protein at pH 6. Ultraviolet second-derivative spectrophotometry, however, suggests an increase in the average number of exposed tyrosine side chains, with 2.25 out of 5 residues exposed for the mutant compared to 1.95 for normal iso-2. Above neutral pH, the protein folds to a mutant conformation possibly related to alkaline cytochrome c. Nuclear Overhauser difference spectroscopy of the reduced nativelike conformation allows assignment of several proton resonances and comparison of side-chain conformations of the heme ligand Met-80 in the mutant and the normal proteins. The proton chemical shifts for the assigned resonances are the same within errors for Gly-76 iso-2 and normal iso-2 at pD 6, 20 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1988

Replacement of a conserved proline eliminates the absorbance-detected slow folding phase of iso-2-cytochrome c.

As a test of the proline isomerization model, we have used oligonucleotide site-directed mutagenesis to construct a mutant form of iso-2-cytochrome c in which proline-76 is replaced by glycine [Wood, L. C., Muthukrishnan, K., White, T. B., Ramdas, L., & Nall, B. T. (1988) Biochemistry (preceding paper in this issue)]. For the oxidized form of Gly-76 iso-2, an estimate of stability by guanidine hydrochloride induced unfolding indicates that the mutation destabilizes the protein by 1.2 kcal/mol under standard conditions of neutral pH and 20 degrees C (delta G degrees u = 3.8 kcal/mol for normal Pro-76 iso-2 versus 2.6 kcal/mol for Gly-76 iso-2). The kinetics of folding/unfolding have been monitored by fluorescence changes throughout the transition region using stopped-flow mixing. The rates for fast and slow fluorescence-detected refolding are unchanged, while fast unfolding is increased in rate 3-fold in the mutant protein compared to normal iso-2. A new kinetic phase in the 1-s time range is observed in fluorescence-detected unfolding of the mutant protein. The presence of the new phase is correlated with the presence of species with an altered folded conformation in the initial conditions, suggesting assignment of the phase to unfolding of this species. The fluorescence-detected and absorbance-detected slow folding phases have been monitored as a function of final pH by manual mixing between pH 5.5 and 8 (0.3 M guanidine hydrochloride, 20 degrees C).(ABSTRACT TRUNCATED AT 250 WORDS)

Cytochrome c Group↗