Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins

The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D₂O medium supplemented with either labeled α-ketoisovalerate for the labeling of the four prochiral methyl groups or with 2-acetolactate for the stereospecific labeling of the valine and leucine side chains. However, when these labeling schemes are applied to large protein assemblies, significant overlap between the correlations of the valine and leucine methyl groups occurs, hampering the analysis of 2D methyl-TROSY spectra. Analysis of the leucine and valine biosynthesis pathways revealed that the incorporation of labeled precursors in the leucine pathway can be inhibited by the addition of exogenous l-leucine-d₁₀. We exploited this property to label stereospecifically the pro-R and pro-S methyl groups of valine with minimal scrambling to the leucine residues. This new labeling protocol was applied to the 468 kDa homododecameric peptidase TET2 to decrease the complexity of its NMR spectra. All of the pro-S valine methyl resonances of TET2 were assigned by combining mutagenesis with this innovative labeling approach. The assignments were transferred to the pro-R groups using an optimally labeled sample and a set of triple resonance experiments. This improved labeling scheme enables us to overcome the main limitation of overcrowding in the NMR spectra of prochiral methyl groups, which is a prerequisite for the site-specific measurement of the structural and dynamic parameters or for the study of interactions in very large protein assemblies.     

Selective editing of Val and Leu methyl groups in high molecular weight protein NMR

The development of methyl-TROSY approaches and specific (13)C-(1)H labeling of Ile, Leu and Val methyl groups in highly deuterated proteins has made it possible to study high molecular weight proteins, either alone or in complexes, using solution nuclear magnetic resonance (NMR) spectroscopy. Here we present 2-dimensional (2D) and 3-dimensional (3D) NMR experiments designed to achieve complete separation of the methyl resonances of Val and Leu, labeled using the same precursor, α-ketoisovalerate or acetolactate. The 2D experiment can further select the methyl resonances of Val or Leu based on the C(α) or C(β) chemical shift values of Val or Leu, respectively. In the 3D spectrum, the methyl cross peaks of Val and Leu residues have opposite signs; thus, not only can the residue types be easily distinguished, but the methyl pairs from the same residue can also be identified. The feasibility of this approach, implemented in both 2D and 3D experiments, has been demonstrated on an 82 kDa protein, malate synthase G. The methods developed in this study will reduce resonance overlaps and also facilitate structure-guided resonance assignments.     

Separate regulation of transport and biosynthesis of leucine, isoleucine, and valine in bacteria.

Since both transport activity and the leucine biosynthetic enzymes are repressed by growth on leucine, the regulation of leucine, isoleucine, and valine biosynthetic enzymes was examined in Escherichia coli K-12 strain EO312, a constitutively derepressed branched-chain amino acid transport mutant, to determine if the transport derepression affected the biosynthetic enzymes. Neither the iluB gene product, acetohydroxy acid synthetase (acetolactate synthetase, EC 4.1.3.18), NOR THE LEUB gene product, 3-isopropylmalate dehydrogenase (2-hydroxy-4-methyl-3-carboxyvalerate-nicotinamide adenine dinucleotide oxido-reductase, EC 1.1.1.85), were significantly affected in their level of derepression or repression compared to the parental strain. A number of strains with alterations in the regulation of the branched-chain amino acid biosynthetic enzymes were examined for the regulation of the shock-sensitive transport system for these amino acids (LIV-I). When transport activity was examined in strains with mutations leading to derepression of the iluB, iluADE, and leuABCD gene clusters, the regulation of the LIV-I transport system was found to be normal. The regulation of transport in an E. coli strain B/r with a deletion of the entire leucine biosynthetic operon was normal, indicating none of the gene products of this operon are required for regulation of transport. Salmonella typhimurium LT2 strain leu-500, a single-site mutation affecting both promotor-like and operator-like function of the leuABCD gene cluster, also had normal regulation of the LIV-I transport system. All of the strains contained leucine-specific transport activity, which was also repressed by growth in media containing leucine, isoleucine and valine. The concentrated shock fluids from these strains grown in minimal medium or with excess leucine, isoleucine, and valine were examined for proteins with leucine-binding activity, and the levels of these proteins were found to be regulated normally. It appears that the branched-chain amino acid transport systems and biosynthetic enzymes in E. coli strains K-12 and B/r and in S. typhimurium strain LT2 are not regulated together by a cis-dominate type of mechanism, although both systems may have components in common.     

13C-detected HN(CA)C and HMCMC experiments using a single methyl-reprotonated sample for unambiguous methyl resonance assignment

Methyl groups provide an important source of structural and dynamic information in NMR studies of proteins and their complexes. For this purpose sequence-specific assignments of methyl 1H and 13C resonances are required. In this paper we propose the use of 13C-detected 3D HN(CA)C and HMCMC experiments for assignment of methyl 1H and 13C resonances using a single selectively methyl protonated, perdeuterated and 13C/15N-labeled sample. The high resolution afforded in the 13C directly-detected dimension allows one to rapidly and unambiguously establish correlations between backbone HN strips from the 3D HN(CA)C spectrum and methyl group HmCm strips from the HMCMC spectrum by aligning all possible side-chain carbon chemical shifts and their multiplet splitting patterns. The applicability of these experiments for the assignment of methyl 1H and 13C resonances is demonstrated using the 18.6 kDa B domain of the Escherichia coli mannose transporter (IIBMannose).     

The dissimilation of leucine, isoleucine and valine to volatile fatty acids by adult Fasciola hepatica

The dissimilation of leucine, isoleucine and valine to volatile fatty acids was determined in Fasciola hepatica and the degradation of (U−¹⁴C) branched amino acids to the volatile fatty acids end products demonstrated. F. hepatica was found to metabolize leucine, isoleucine and valine to isovaleric, 2-methylbutyric and isobutyric acid respectively. The rate of formation of isobutyrate, isovalerate and 2-methylbutyrate was found to be positively related to the rate of propionic acid production with air or nitrogen as the gas phase. However, under 95% O₂/5% CO₂ the formation of the branched chain acids was independent of propionic acid production. The production of isobutyrate, isovalerate and 2-methylbutyrate caused a simultaneous reduction in the rate of acetate formation. The role of propionate formation in regulating metabolism is discussed.     

Development of cancer vaccines using autologous and recombinant high molecular weight stress proteins

High molecular weight heat shock proteins (HSPs), hsp110 and grp170, derived from cancer cells have been previously shown to elicit tumor-specific immunity. This phenomenon is attributed to the antigenic peptides associated with the HSPs. Based on the unique chaperoning properties of these HSPs, a new vaccination strategy has been recently developed to elicit antigen-specific antitumor immunity. This approach utilizes tumor-associated antigens naturally complexed to these highly efficient molecular chaperones under heat shock conditions. This chapter focuses on the methodologies of these two vaccine strategies: I. purification of hsp110 and grp170 from tumor tissue or cell lines; II. generation and characterization of in vitro HSP-antigen complexes by heat shock using recombinant HSPs derived from a baculovirus protein expression system.     

Susceptibility behaviour and specific heat anomaly in single crystals of alanine and valine

Magnetization of single crystals ofD-,L-alanine andD-valine were measured as a function of temperature using the SQUID magnetometer. An obvious lambda transition at 270 ± 1 K was shown in the specific heat measurement of alanine and valine enantiomers by differential scanning calorimetry (DSC). Magnetic transition temperature seems coincident with that of lambda transition. Temperature dependence of the X-ray powder diffraction forD-valine showed no crystal lattice change under the temperature cooling down from 293 K to 123 K. We propose that the difference of theX T curve between theD-alanine andL-alanine is attributable to the variation of intramolecular geometry of chirality density in the presence of an external magnetic field. The chirality characteristics of alanine and valine enantiomers by the specific heat and susceptibility behaviour are discussed.     

A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins

A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[¹³C]glucose and subsaturating amounts of 2-[¹³C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional ¹H-¹³C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NMR assignments of prochiral methyl groups.     

Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease.

This paper describes the application of recently developed nuclear magnetic resonance (NMR) pulse sequences to obtain information about the internal dynamics of isotopically enriched hydrophobic side chains in proteins. The two-dimensional spectra provided by the pulse sequences enable one to make accurate measurements of nuclear Overhauser effects (NOE) and longitudinal (T1) and transverse (T2) relaxation times of enriched methyl carbons in proteins. Herein, these techniques are used to investigate the internal dynamics of the 11 leucine side chains of staphylococcal nuclease (SNase), a small enzyme having Mr = 16.8K, in the absence and presence of ligands thymidine 3',5'-bisphosphate (pdTp) and Ca2+. We report the synthesis of [5,5'-13C2]leucine, the preparation of SNase containing the labeled leucine, the sequential assignment of the leucine methyl carbons and protons in the liganded and unliganded proteins, and the measurement of the 13C T1, T2, and NOE values for the SNase leucine methyl carbons. Analysis of the relaxation parameters using the formalism of Lipari and Szabo shows that the internal motions of the leucine methyl carbons are characterized by effective correlation times tau f (5-80 ps) and tau s (less than 2 ns). The fast motion is identified with the rapid rotation of the methyl group about the C gamma-C delta bond axis, while the slow motion is associated with reorientation of the C gamma-C delta bond axis itself. The mean squared order parameters associated with the latter motion, Ss2, lie in the range 0.34-0.92. The values of Ss2 correlate reasonably well with the temperature factors of the leucine methyl carbons obtained from the crystal structures, but some are smaller than anticipated on the basis of the fact that nearly all leucine methyl carbons are buried and have temperature factors no larger than that of the leucine backbone atoms. Five leucine residues in liganded SNase and eight in unliganded SNase have values of Ss2 less than 0.71. These order parameters correspond to large amplitude motions (angular excursions of 27-67 degrees) of the C gamma-C delta bond axis. These results indicate that, in solution, the internal motions of the leucine side chains of SNase are significantly larger than suggested by the X-ray structures or by qualitative analysis of NOESY spectra. Comparison of Ss2 values obtained from liganded and unliganded SNase reveals a strong correlation between delta Ss2 and distance between the leucine methyl carbon and the ligands.(ABSTRACT TRUNCATED AT 400 WORDS)     

Utilization of serine, leucine, isoleucine, and valine by Thermoanaerobacter brockii in the presence of thiosulfate or Methanobacterium sp. as electron acceptors

Thermoanaerobacter brockii fermented serine to acetate and ethanol. It oxidized leucine to isovalerate, isoleucine to 2-methylbutyrate, and valine to isobutyrate only in the presence of thiosulfate, or when co-cultured with Methanobacterium sp. This oxidative deamination was rendered thermodynamically possible by the ability ofT. brockii to reduce thiosulfate to sulfide or the transfer of reducing equivalents to the hydrogenotrophic methanogen. The results suggest that T. brockii may be of ecological significance in thermal environments in the turnover of amino acids, especially with thiosulfate or H(2)-utilizing methanogens are present.     

Detection of staphylococcus aureus infection by enzyme-linked immunosorbent assay and immunoblotting, using high molecular weight staphylococcal proteins

Abstract Two high molecular weight staphylococcal proteins, fibronectin-binding protein and a M _τ 200 000 protein, were investigated as antigens for serodiagnosis of staphylococcal infections. Sera from patients with staphylococcal infections and from controls were subjected to immunoblot analysis with staphylococcal lysate proteins to identify staphylococcal antigens to which patients with staphylococcal infections specifically exhibited antibodies. On such protein was found in the M _τ 200 000 region. This protein was purified and used as antigen in ElISA and compared with other antigens, namely fibronectin-binding protein(s) (FNBP, M _τ , 185 000), α-toxin and teichoic acid. Sera from patients with staphylococcal infections contained antibodies to the high molecular weight proteins in higher titers than sera from patients with non-staphylococcal infections or healthy subjects. Based on their amino-acid compositions and different abilities to bind fibronectin it was concluded that the M _τ 200 000 protein and FNBP were not identical.     

Effects of leucine supplementation on muscle protein synthesis and degradation pathways in broilers at constant dietary concentrations of isoleucine and valine

The present study investigated the hypothesis that dietary concentrations of leucine (Leu) in excess of the breeder´s recommendations activates protein synthesis and decreases protein degradation in muscle of broilers. Day-old male Ross 308 broilers (n = 450) were phase-fed corn-soybean meal-based diets during starter (d 1–10), grower (d 11–22), and finisher (d 23–34) period. The basal diets fed to the control group (L0) met the broilers’ requirements for nutrients and amino acids, and contained Leu, Leu:isoleucine (Ile) and Leu:valine (Val) ratios, close to those recommended by the breeder (Leu:Ile: 100:54, 100:52, 100:51; Leu:Val 100:64, 100:61, 100:58; in starter, grower and finisher diet, resp.). Basal diets were supplemented with Leu to exceed the breeder’s recommendations by 35% (group L35) and 60% (group L60). Growth performance during 34 d, and carcass weights, and breast and thigh muscle weights on d 34 were similar among groups. Hepatic and muscle mRNA levels of genes involved in the somatotropic axis [growth hormone receptor, insulin-like growth factor (IGF)-1, IGF binding protein 2, IGF receptor] on d 34 were not influenced by Leu. In the breast muscle, relative mRNA abundances of genes involved in the mammalian target of rapamycin (mTOR) pathway of protein synthesis (mTOR, ribosomal p70 S6 kinase) and the ubiquitin-proteasome pathway of protein degradation (F-box only protein 32, Forkhead box protein O1, Muscle RING-finger protein-1) on d 34 were largely similar among groups. Likewise, relative phosphorylation and thus activation of mTOR and ribosomal protein S6 involved in the mTOR pathway, and of eukaryotic translation initiation factor 2A (eIF2a) involved in the general control nonderepressible 2 (GCN2)/eIF2a pathway of protein synthesis inhibition, were not influenced. These data indicate that dietary Leu concentrations exceeding the broiler´s requirements up to 60% neither influence protein synthesis nor degradation pathways nor muscle growth in growing broilers.