Bridging the gap: A set of selective 1H-15N-correlations to link sequential neighbors of prolines

Triple-resonance experiments are standard in the assignment of protein spectra. Conventional assignment strategies use ¹H-¹⁵N-correlations as a starting point and therefore have problems when proline appears in the amino acid sequence, which lacks a signal in these correlations. Here we present a set of amino acid selective pulse sequences which provide the information to link the amino acid on either side of proline residues and thus complete the sequential assignment. The experiments yield amino acid type selective ¹H-¹⁵N-correlations which contain signals from the amino protons of the residues either preceding or following proline in the amino acid sequence. These protons are correlated with their own nitrogen or with that of the proline. The new experiments are recorded as two-dimensional experiments and their performance is demonstrated by application to a 115-residue protein domain.     

Backbone NMR resonance assignment of the catalytic subunit of cAMP-dependent protein kinase A in complex with AMP-PNP

The catalytic subunit of protein kinase A is involved with a number of signal transduction pathways and has been used as a benchmark to study the structural biology and biochemistry for the entire kinase family of enzymes. Here, we report the backbone assignment of the intact 41 kDa catalytic subunit bound to AMP-PNP. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Systematic relationships of the ranunculacea based on amino acid sequence data

Plastocyanin partial amino acid sequences (40 residues) of five members of the Ranunculaceae were used, together with many other flowering plant plastocyanin sequences already published, to construct dendrograms. On this basis the Ranunculaceae appear more closely related to the Rosaceae and Fabaceae than to the other families investigated. Dendograms constructed from amino acid sequence data and serological data of five members of the Ranunculaceae were similar.     

Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure.

The conditional probability, P(sigma/x), is a statement of the probability that the value of sigma will be found given the prior information that a value of x has been observed. Here sigma represents any one of the secondary structure types, alpha, beta, tau, and rho for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P alpha, for sheet, P beta, and for turn, P tau; and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I alpha, for sheet, I beta, for turn, I tau, and for random structure, I rho. Plots of P(sigma/x) vs. x are demonstrated to provide information about the correlation between structure and attribute, sigma and x. The separations between different P(sigma/x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P(alpha/x), P(beta/x), P(tau/x) and P(rho/x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix greater than P alpha much greater than N-cap greater than C-cap approximately I alpha approximately I tau. The information value for turns, I tau, was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I beta much greater than P beta approximately hydropathy greater than I rho approximately hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I alpha approximately P alpha approximately hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P beta much greater than I rho approximately hydropathy. Indications of the absence of sigma could be as useful for some applications as the indication of the presence of sigma.     

Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques

One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where thepeaks in the spectra are assigned to specific spins within specificresidues. In this paper, we discuss a spin system assignment tool based onpattern recognition techniques. This tool employs user-specified templatesto search for patterns of peaks in the original spectra; these patterns maycorrespond to side-chain or backbone fragments. Multiple spectra willnormally be searched simultaneously to reduce the impact of noise. Thesearch generates a preliminary list of putative assignments, which arefiltered by a set of heuristic algorithms to produce the final results list.Each result contains a set of chemical shift values plus information aboutthe peaks found. The results may be used as input for combinatorialroutines, such as sequential assignment procedures, in place of peak lists.Two examples are presented, in which (i) HCCH-COSY and -TOCSY spectra arescanned for side-chain spin systems; and (ii) backbone spin systems aredetected in a set of spectra comprising HNCA, HN(CO)CA, HNCO, HN(CA)CO,CBCANH and CBCA(CO)NH.     

Highly selective recognition of L‐phenylalanine with molecularly imprinted polymers based on imidazolyl amino acid chiral ionic liquid

Several amino acid chiral ionic liquids were introduced as functional monomers to prepare molecularly imprinted polymers for specific recognition of L‐phenylalanine. Among them, the imprinted polymers L‐Phe@MIPs based on [ViImC3][L‐Pro] showed the best selective recognition ability for L‐phenylalanine. A series of experiments such as dynamic adsorption, static adsorption, and competitive adsorption were conducted to investigate the specific recognition ability and adsorption capacity of the L‐Phe@MIPs. It is found that the adsorption efficiency to L‐phenylalanine on L‐Phe@MIPs was 3.11 times higher than that to D‐phenylalanine. All the results demonstrated that the L‐Phe@MIPs possessed good recognition and relatively high adsorption efficiency for L‐phenylalanine. Besides, the recovery of L‐phenylalanine was above 98%, and the L‐Phe@MIPs exhibited good reusability.     

1-<Superscript>13</Superscript>C amino acid selective labeling in a <Superscript>2</Superscript>H<Superscript>15</Superscript>N background for NMR studies of large proteins

Isotope labeling by residue type (LBRT) has long been an important tool for resonance assignments at the limit where other approaches, such as triple-resonance experiments or NOESY methods do not succeed in yielding complete assignments. While LBRT has become less important for small proteins it can be the method of last resort for completing assignments of the most challenging protein systems. Here we present an approach where LBRT is achieved by adding protonated ¹⁴N amino acids that are ¹³C labeled at the carbonyl position to a medium for uniform deuteration and ¹⁵N labeling. This has three important benefits over conventional ¹⁵N LBRT in a deuterated back ground: (1) selective TROSY-HNCO cross peaks can be observed with high sensitivity for amino-acid pairs connected by the labeling, and the amide proton of the residue following the ¹³C labeled amino acid is very sharp since its alpha position is deuterated, (2) the ¹³C label at the carbonyl position is less prone to scrambling than the ¹⁵N at the α-amino position, and (3) the peaks for the 1-¹³C labeled amino acids can be identified easily from the large intensity reduction in the ¹H-¹⁵N TROSY-HSQC spectrum for some residues that do not significantly scramble nitrogens, such as alanine and tyrosine. This approach is cost effective and has been successfully applied to proteins larger than 40 kDa. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A defined medium for and the effect of insulin on the growth,amino acid transport,and morphology of chinese hamster ovary cells,CHO-K1 (CCL 61) and the isolation of insulin “independent” mutants

Summary Insulin, FeSO₄, or transferrin are major requirements together with HEPES buffer and selenium for the growth of CHO-K1 (CCL 61) in a modified F12 medium (M-F12). Insulin stimulates growth at 1 ng/ml to 10 μg/ml. In the defined medium minus insulin, CHO-K1 grows slowly as elongated, elliptical cells in parallel arrays typical of normal diploid fibroblasts in contrast to round-to-cuboid cells in loosely overlapping arrays in the presence of serum or insulin. During prolonged incubation in the absence of insulin the cells gather up into a large spherical cluster of viable cells. Insulin “independent” mutants have been isolated whose growth rate during exponential phase in the absence of insulin (48 h to 84 or 96 hrs) is 2.7 to 3.6 times that of the parental culture. Insulin stimulates the growth of these variants only during the first 48 h and is inhibitory at 50 to 500 ng/ml during the exponential phase. Insulin induction of the A system of amino acid transport occurs in about 8 h and requires both protein and RNA synthesis. This work was supported in part by National Science Foundation Grant PCM 7903242 and by the University of California.     

Dopamine differentially induces aggregation of A53T mutant and wild type alpha-synuclein: insights into the protein chemistry of Parkinson's disease

Aggregation of α-synuclein is known to be a causal factor in the genesis of Parkinson’s disease and Dementia with Lewy bodies. Duplication and/or triplication and mutation of the α-synuclein gene are associated with sporadic and familial Parkinson’s disease. Synucleinopathies appear to primarily affect dopaminergic neurons. The present studies investigate the role of dopamine in α-synuclein aggregation through NMR. Dopamine causes aggregation of both wild type and A53T mutant α-synuclein in a temperature-dependent manner, but the mutant A53T shows a greater propensity to aggregate in the presence of dopamine only at 37 °C. A single point mutation in the α-synuclein A53T mutant gene results in a structural change in the protein and drastically increases its propensity to aggregate in the presence of dopamine. The present data indicate that mutation in the α-synuclein gene may predispose the protein to dopamine-induced aggregation, thereby contributing to disease pathogenesis.     

Essential amino acid residues in the central transmembrane domains and loops for energy coupling of Streptomyces coelicolor A3(2) H-pyrophosphatase

The H⁺-translocating inorganic pyrophosphatase is a proton pump that hydrolyzes inorganic pyrophosphate. It consists of a single polypeptide with 14−17 transmembrane domains, and is found in a range of organisms. We focused on the second quarter region of Streptomyces coelicolor A3(2) H⁺-pyrophosphatase, which contains long conserved cytoplasmic loops. We prepared a library of 1536 mutants that were assayed for pyrophosphate hydrolysis and proton translocation. Mutant enzymes with low substrate hydrolysis and proton-pump activities were selected and their DNAs sequenced. Of these, 34 were single-residue substitution mutants. We generated 29 site-directed mutant enzymes and assayed their activity. The mutation of 10 residues in the fifth transmembrane domain resulted in low coupling efficiencies, and a mutation of Gly¹⁹⁸ showed neither hydrolysis nor pumping activity. Four residues in cytoplasmic loop e were essential for substrate hydrolysis and efficient H⁺ translocation. Pro¹⁸⁹, Asp²⁸¹, and Val³⁵¹ in the periplasmic loops were critical for enzyme function. Mutation of Ala³⁵⁷ in periplasmic loop h caused a selective reduction of proton-pump activity. These low-efficiency mutants reflect dysfunction of the energy-conversion and/or proton-translocation activities of H⁺-pyrophosphatase. Four critical residues were also found in transmembrane domain 6, three in transmembrane domain 7, and five in transmembrane domains 8 and 9. These results suggest that transmembrane domain 5 is involved in enzyme function, and that energy coupling is affected by several residues in the transmembrane domains, as well as in the cytoplasmic and periplasmic loops. H⁺-pyrophosphatase activity might involve dynamic linkage between the hydrophilic and transmembrane domains.