Sequence‐specific determination of protein and peptide concentrations by absorbance at 205 nm

Quantitative studies in molecular and structural biology generally require accurate and precise determination of protein concentrations, preferably via a method that is both quick and straightforward to perform. The measurement of ultraviolet absorbance at 280 nm has proven especially useful, since the molar absorptivity (extinction coefficient) at 280 nm can be predicted directly from a protein sequence. This method, however, is only applicable to proteins that contain tryptophan or tyrosine residues. Absorbance at 205 nm, among other wavelengths, has been used as an alternative, although generally using absorptivity values that have to be uniquely calibrated for each protein, or otherwise only roughly estimated. Here, we propose and validate a method for predicting the molar absorptivity of a protein or peptide at 205 nm directly from its amino acid sequence, allowing one to accurately determine the concentrations of proteins that do not contain tyrosine or tryptophan residues. This method is simple to implement, requires no calibration, and should be suitable for a wide range of proteins and peptides.     

Measurement of intracellular pH in hamster diaphragm by absorption spectrophotometry

The regulation of intracellular pH (pHi) is important in controlling muscle contraction. In these experiments, a spectrophotometric method of determining pHi was developed, and the method was then used to study muscle pHi regulation during CO2-induced changes in extracellular pH (pHb). Studies were performed in vitro on 27 diaphragm muscle strips obtained from adult hamsters. pHi was measured from the ratio of the absorbances of the acid (lambda = 530 nm) and alkaline (lambda = 460 nm) forms of a vital dye, neutral red, using the unstained diaphragm spectrum as a reference blank. A standard neutral red calibration curve constructed from eight diaphragm muscle homogenates indicated that the absorbance ratio was highly linear, with pH over the range 6.00-8.00. In intact muscle strips gassed with 95% O2-5% CO2, pHb was 7.45 +/- 0.03 (SE) and pHi was 7.00 +/- 0.01 (SE). When the muscle was aerated with CO2 concentrations from 3 to 30%, pHb and pHi changed rapidly and reached a steady state in 10-15 min. However, when pHb ranged from 6.80-7.80, pHi changed little from the value observed when pHb was 7.40. When pHb was less than 6.80 or greater than 7.80, changes in pHi and pHb were quantitatively similar. The results suggest that, in the isolated diaphragm, overall pHi is stable and effectively buffered over a wide range of CO2-induced changes in buffer solution pH.     

Imaging protein structure in water at 2.7 nm resolution by transmission electron microscopy

We demonstrate an in situ transmission electron microscopy technique for imaging proteins in liquid water at room temperature. Liquid samples are loaded into a microfabricated environmental cell that isolates the sample from the vacuum with thin silicon nitride windows. We show that electron micrographs of acrosomal bundles in water are similar to bundles imaged in ice, and we determined the resolution to be at least 2.7 nm at doses of ～35 e/Ų. The resolution was limited by the thickness of the window and radiation damage. Surprisingly, we observed a smaller fall-off in the intensity of reflections in room-temperature water than in 98 K ice. Thus, our technique extends imaging of unstained and unlabeled macromolecular assemblies in water from the resolution of the light microscope to the nanometer resolution of the electron microscope. Our results suggest that real-time imaging of protein dynamics is conceptually feasible.     

Measurement and calibration of peptide group hydrogen-deuterium exchange by ultraviolet spectrophotometry.

An exceedingly simple and convenient method is described for measuring the hydrogen-deuterium exchange behavior of peptide bond-containing molecules by ultraviolet spectrophotometry. The exchange reaction is initiated by diluting a sample from H₂O into D₂O, or the reverse, and can be followed by an easily observable optical density change in the region of peptide absorbance. The method, unlike infrared and magnetic resonance approaches, requires only small amounts of material and, unlike the tritium-Sephadex method, is not restricted to the study of large molecules. Calibrations are provided for exchange rate as a function of pD and temperature and for the change in absorbance per mole peptide group. With this information, the exchange curve to be expected for any peptide group exposed to solvent can be predicted. Comparison with the measured data can then identify peptide-group hydrogen bonding and can also give a measure of the stability of the hydrogen-bonded structure.     

Phosphorylation of human glutamine:fructose-6-phosphate amidotransferase by cAMP-dependent protein kinase at serine 205 blocks the enzyme activity

Glutamine:fructose-6-phosphate amidotransferase (GFAT) is the rate-limiting enzyme in glucosamine synthesis. Prior studies from our laboratory indicated that activation of adenylate cyclase was associated with depletion of O-GlcNAc modification. This finding and evidence that human GFAT (hGFAT) might be regulated by cAMP-dependent protein kinase (PKA) led us to investigate the role of PKA in hGFAT function. We confirmed that adenylate cyclase activation by forskolin results in diminished O-GlcNAc modification of several cellular proteins which can be overcome by exposure of the cells to glucosamine but not glucose, suggesting the PKA activation results in depletion of UDP-GlcNAc for O-glycosylation. To determine if GFAT is indeed regulated by PKA, we expressed the active form of the enzyme using a vaccinia virus expression system and showed that the activity of the enzyme was to decrease to undetectable levels by PKA phosphorylation. We mapped the PKA phosphorylation sites with the aid of matrix-assisted laser desorption ionization mass spectroscopy and showed that the protein was stoichiometrically phosphorylated at serine 205 and also phosphorylated, to a lesser extent at serine 235. Mutagenesis studies indicated that the phosphorylation of serine 205 by PKA was necessary for the observed inhibition of enzyme activity while serine 235 phosphorylation played no observable role. The activity of GFAT is down-regulated by cAMP, thus placing regulation on the hexosamine pathway that is in concert with the energy requirements of the organism. During starvation, hormones acting through adenylate cyclase could direct the flux of glucose metabolism into energy production rather than into synthetic pathways that require hexosamines.     

Crystal structure of pokeweed antiviral protein from seeds ofPhytolacca americana at 0.25 nm

Crystals of pokeweed antiviral protein (PAP) from seeds ofPhytolacca americana with high diffraction ability were grown from high protein concentration (100 mg/mL) solution at high temperature (33°C). The crystal structure was solved by use of molecular replacement method and refied by use of molecular dynamic method at 0.25 nm to anR factor of 18.15% with standard deviations from standard geometry of 0.001 6 nm and 2.04 for bond lengths and bond angles, respectively. Comparison with two other PAPS revealed, near the active center, a sequence- and structure-variable region, consisting of the loop connecting the fifth β-strand with the second α-helix and including a proposed active residue, suggesting this loop probably to be related to difference in activity.     

Revisiting absorbance at 230 nm as a protein unfolding probe

Thermodynamic stability and unfolding kinetics of proteins are typically determined by monitoring protein unfolding with spectroscopic probes, such as circular dichroism (CD) and fluorescence. UV absorbance at 230 nm (A₂₃₀) is also known to be sensitive to protein conformation. However, its feasibility for quantitative analysis of protein energetics has not been assessed. Here we evaluate A₂₃₀ as a structural probe to determine thermodynamic stability and unfolding kinetics of proteins. By using Escherichia coli maltose binding protein (MBP) and E. coli ribonuclease H (RNase H) as our model proteins, we monitored their unfolding in urea and guanidinium chloride with A₂₃₀. Significant changes in A₂₃₀ were observed with both proteins on unfolding in the chemical denaturants. The global stabilities were successfully determined by measuring the change in A₂₃₀ in varying concentrations of denaturants. Also, unfolding kinetics was investigated by monitoring the change in A₂₃₀ under denaturing conditions. The results were quite consistent with those determined by CD. Unlike CD, A₂₃₀ allowed us to monitor protein unfolding in a 96-well microtiter plate with a UV plate reader. Our finding suggests that A₂₃₀ is a valid and convenient structural probe to determine thermodynamic stability and unfolding kinetics of proteins with many potential applications.     

Crystal structure of pokeweed antiviral protein from seeds of Phytolacca americana at 0.25 nm

ＡｔｖａｒｉｏｕｓｄｅｖｅｌｏｐｉｎｇｓｔａｇｅｓｔｈｅｄｉｆｆｅｒｅｎｔｔｉｓｓｕｅｓｏｆＰ.ａｍｅｒｉｃａｎａ(ｐｏｋｅｗｅｅｄ)ｃａｎｓｙｎｔｈｅｓｉｚｅａｃｌａｓｓｏｆｉｓｏｚｙｍｅｓｗｉｔｈｔｈｅａｂｉｌｉｔｙｔｏｉｎｈｉｂｉｔｔｈｅｐｒｏｌｉｆｅｒａｔｉｏｎｏｆｖｉｒｕｓ.ＴｈｉｓａｂｉｌｉｔｙｌｅａｄｓｔｏｔｈｅｄｉｓｃｏｖｅｒｙａｎｄｎａｍｅｏｆＰＡＰｓ[1—4].ＤｉｆｆｅｒｅｎｔＰＡＰｓｈａｖｅｂｅｅｎｆｏｕｎｄｆｒｏｍｌｅａｖｅｓ(ＰＡＰ)[1],ｓｕｍｍｅｒｌｅａｖｅｓ(ＰＡＰＩＩ)[2],…     

Crystal structure of pokeweed antiviral protein from seeds of Phytolacca americana at 0.25 nm

Crystals of pokeweed antiviral protein (PAP) from seeds of Phytolacca americana with high diffraction ability were grown from high protein concentration (100 mg/mL) solution at high temperature (33℃). The crystal structure was solved by use of molecular replacement method and refined by use of molecular dynamic method at 0 25 nm to an R factor of 18.15% with standard deviations from standard geometry of 0.001 6 nm and 2.04° for bond lengths and bond angles, respectively. Comparison with two other PAPs revealed, near the active center, a sequence and structure variable region, consisting of the loop connecting the fifth β strand with the second α helix and including a proposed active residue, suggesting this loop probably to be related to difference in activity.$$$$     

Measurement of protein concentration by quantitative electron microscopy

The method of quantitative electron microscopy was applied to the measurement of protein concentration in thin sections. The human erythrocyte was selected as a model because of its apparently uniform protein concentration. Phosphotungstic acid (PTA) in aqueous solution was used as a reversible stain for protein, and PTA-stained Dowex resin spheres were embedded along with the red cells as standards for measurement of section thickness. The mass of stain removed from a given area of sectioned red cell by buffer (pH 7.4) was measured by quantitative electron microscopy. From the stoichiometry of the reaction between PTA and red cell protein established in this study, the amount of protein present in the measured area was calculated. From this amount of protein and the measured thickness, the concentration of protein was calculated and expressed as g/100 ml, for comparison with the clinical laboratory value for hemoglobin. Groups of red cells from the same sample were measured on 3 different days and their mean values (g/100 ml ± SD) were 29 ± 3.9, 30 ± 2.7, and 33 ± 4.6, compared to the clinical laboratory value of 32.1 g/100 ml packed cells, after correction for volume change and protein loss during fixation.     

Measurement of protein surface shape by solid angles

A method for measuring the gross shape of local regions of protein surface is presented and applied to an examination of three proteins. Any point on the protein surface can be assigned a number that measures the degree of convexity or concavity of the surface in the vicinity of the point. This number is computed by centring a sphere at that point and measuring how much of the sphere lies inside the protein. The sphere radius is a parameter chosen according to the scale of the features that are being analysed. The amount of sphere intersecting the protein is interpreted as a solid angle, denoted omega. Three proteins are analysed by this method: lysozyme, Superoxide dismutase and chymotrypsin. The resulting omega values are used to colour code the protein surfaces displayed on a colour raster graphics terminal. The method can be seen to reliably identify protrusions and depressions. The difficulty of developing a generally useful method for measuring protein surface shape is discussed. Possible applications of the solid-angle method include the analysis of shape complementarity at protein interfaces, the development of computer algorithms for predicting complexes between proteins, or between proteins and ligands, the identification of homologous epitopes on different proteins that might be immunologically crossreactive, and the determination of correlations between surface geometry and chemical properties.     

Measurement of cystic fibrosis transmembrane conductance regulator activity using fluorescence spectrophotometry

Cystic fibrosis (CF) is a frequent autosomal recessive disease caused by mutations that impair the CF transmembrane conductance regulator (CFTR) protein function. CFTR is a chloride channel activated by cyclic AMP (cAMP) via protein kinase A (PKA) and ATP hydrolysis. We describe here a method to measure CFTR activity in a monolayer of cultured cells using a fluorescence spectrophotometer and the chloride-sensitive probe 6-methoxy-N-(3-sulfopropyl)quinolinium (SPQ). Modifying a slice holder, the spectrophotometer quartz cuvette was converted in a perfusion chamber, allowing measurement of CFTR activity in real time, in a monolayer of T84 colon carcinoma cells. The SPQ Stern–Volmer constant (K_Cl^-) for chloride in water solution was 115.0 ± 2.8 M⁻¹, whereas the intracellular K_Cl^- was 17.8 ± 0.8 M⁻¹, for T84 cells. A functional analysis was performed by measuring CFTR activity in T84 cells. The CFTR transport inhibitors CFTR(inh)-172 (5 μM) and glibenclamide (100 μM) showed a significant reduction (P < 0.05) in CFTR activity. This simple method allows measuring CFTR activity in a very simple, reproducible, and sensitive way.     

Determination of protein concentration in cleaving mammalian ova by the capillary spectrophotometry method]

A micromodification of the Lowry's method is described which allows to measure reliably the protein content in 5-20 embryos of white rats and CBA mice. Differences in the protein content in rat embryos at the stages of 2 blastomeres and blastocyst were shown to be statistically unreliable (20.2 +/- 1.4 and 18.9 +/- 1.3 ng, resp.). The protein content in the mouse embryos at the same two stages differs reliably (19.1 +/- 1.1 and 22.0 +/- +/- 1.7 ng, resp.). The protein content in zona pellucida does not differ reliably from those in rat embryos both at the stages of 2 blastomeres (4.5 ng) and blastocyst (2.3 ng). The protein content in embryos devoid of zona pellucida decreased after 3 hours incubation in the medium 199 at 37 degrees at the stages of morula and blastocyst by 17-20% in rats and by 50% in mice. Addition of 1% serum albumin to the incubation medium did not prevent the partial "loss" of protein by the embryos. The protein content in the rat and mouse embryos at the stage of 2 blastomeres suffered no changes under long-term incubation in the medium 199.     

Measurement of protein biomass by Fourier transform infrared-photoacoustic spectroscopy

A relatively new analytical technique, Fourier transform infrared-photoacoustic spectroscopy (FTIR-PAS), provides spectra of bacteria, fungi, and other microorganisms in solid states not suitable for conventional absorption spectroscopy. In this paper the feasibility of quantitative measurement of protein biomass on solid substrates by FTIR-PAS is examined and discussed. By measuring photoacoustic absorption bands from amide groups in the protein of microorganisms, the increase in biomass that occurs during growth was monitored directly and accurately. Incorporation of polyacrylonitrile into the sample as an internal standard was shown to be a convenient method for improving both the reliability and the range of detection by photoacoustic spectroscopy. Results of FTIR-PAS measurements of known quantities of microbial mass in simulated growth experiments suggest that the technique may be especially suitable for assays of microorganisms used in solid-state biosyntheses of drugs, hormones, and other biological agents.     

Vitamin D-interacting protein 205 (DRIP205) coactivation of estrogen receptor alpha (ERalpha) involves multiple domains of both proteins

Vitamin D-interacting protein 205 (DRIP205) is a mediator complex protein that anchors the complex to the estrogen receptor (ER) and other nuclear receptors (NRs). In ZR-75 breast cancer cells treated with 17beta-estradiol (E2) and transfected with a construct containing three tandem estrogen responsive elements (pERE(3)), DRIP205 coactivates ERalpha-mediated transactivation. DRIP205Delta587-636 is a DRIP205 mutant in which both NR boxes within amino acids 587-636 have been deleted and, in parallel transfection studies, DRIP205Delta587-636 also coactivates ERalpha. Moreover, both wild-type and variant DRIP205 also colocalize with ERalpha in the nuclei of transfected cells. Extensive deletion analysis of DRIP205 shows that multiple domains of this protein play a role in coactivation of ERalpha and in interactions with ERalpha. Coactivation of ERalpha by DRIP205 does not require NR boxes, and variants with deletion of N-terminal (amino acids 1-639) and C-terminal (amino acids 576-1566) significantly coactivate ERalpha. DRIP205 resembles p160 coactivators that also interact with multiple regions of ERalpha; however, unlike p160 coactivators, DRIP205 coactivation of ERalpha does not require NR boxes.     

An absolute method for protein determination based on difference in absorbance at 235 and 280 nm

Because of the importance of quantitative determination of protein in the research laboratory as well as in the food and feed industries (1), search for the ideal method continues unabated after many years. Methods available include nitrogen determination (Kjeldahl (2) and Dumas (3)), hydrolysis of the protein, derivatization of the amino acids with phthalaldehyde and fluorescence determination (4), determination of bound or free lysine (5) or glutamate (4), and the Lowry (6), biuret (7) dye-binding (8–11) turbidity (12) and spectral methods (13). With the exception of the spectral methods, the methods involve destruction of the sample.In this paper we report the use of difference in absorbance between 235 and 280 nm for determination of protein concentration.