PubMed · 5525571
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M Bufano, F Ronchi. [Hepatic function in renal insufficiency].. https://pubmed.ncbi.nlm.nih.gov/5525571/
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Amino acid (AA) profiles from body fluids such as blood and urine are clinical indicators for diagnosing metabolic and hepatic diseases. Current quantitative methods, such as liquid chromatography-mass spectrometry (LC-MS) with isotopically labelled internal standards (ISs), are costly and technically demanding. This study proposes a cost-efficient alternative using structural isomers as ISs in a direct liquid infusion (DLI) tandem mass spectrometry (MS/MS) approach. The method leverages chimeric spectra and fragment intensity ratios to quantify AAs, demonstrating high linearity and precision even with a 3D ion trap mass analyser. This approach offers a viable strategy for AA quantification in preventive medicine, particularly for screening metabolic diseases such as phenylketonuria, diabetes, and liver dysfunction.
We used a nonredundant set of 621 protein-protein interfaces of known high-resolution structure to derive residue composition and residue-residue contact preferences. The residue composition at the interfaces, in entire proteins and in whole genomes correlates well, indicating the statistical strength of the data set. Differences between amino acid distributions were observed for interfaces with buried surface area of less than 1,000 A(2) versus interfaces with area of more than 5,000 A(2). Hydrophobic residues were abundant in large interfaces while polar residues were more abundant in small interfaces. The largest residue-residue preferences at the interface were recorded for interactions between pairs of large hydrophobic residues, such as Trp and Leu, and the smallest preferences for pairs of small residues, such as Gly and Ala. On average, contacts between pairs of hydrophobic and polar residues were unfavorable, and the charged residues tended to pair subject to charge complementarity, in agreement with previous reports. A bootstrap procedure, lacking from previous studies, was used for error estimation. It showed that the statistical errors in the set of pairing preferences are generally small; the average standard error is approximately 0.2, i.e., about 8% of the average value of the pairwise index (2.9). However, for a few pairs (e.g., Ser-Ser and Glu-Asp) the standard error is larger in magnitude than the pairing index, which makes it impossible to tell whether contact formation is favorable or unfavorable. The results are interpreted using physicochemical factors and their implications for the energetics of complex formation and for protein docking are discussed. Proteins 2001;43:89-102.
Chemokines direct immune cells toward sites of infection by establishing a gradient across the extracellular matrix of the tissue. This gradient is thought to be stabilized by ligation of chemokines to sulfated polysaccharides known as glycosaminoglycans (GAGs) that are found on the surface of endothelial and other cells as well as in the tissue matrix. GAGs interact with chemokines and in some cases cause them to aggregate. The interaction between cell surface GAGs and chemokines has also been postulated to play a role in the anti-HIV activity of some chemokines, including MIP-1beta. Since many proteins interact with GAGs by utilizing basic residues, we mutated R18, K45, R46, and K48 in MIP-1beta to investigate the role of these residues in GAG binding and CCR5 function. We find that no single amino acid substitution alone has a dramatic effect on heparin binding, although change at R46 has a moderate effect. However, binding to heparin is completely abrogated in a mutant (K45A/R46A/K48A) in which the entire "40's loop" has been neutralized. A functional study of these mutants reveals that the charged residues in this 40's loop, particularly K48 and R46, are critical mediators of MIP-1beta binding to its receptor CCR5. However, despite the partially overlapping function of the residues in the 40's loop in binding to both CCR5 and heparin, the presence of cell surface sugars does not appear to be necessary for the ability of MIP-1beta to function on its receptor CCR5, as enzymatic removal of GAGs from cells results in little effect on MIP-1beta activity. Because the means by which the chemokine gradient transmits information to the recruited cells is not well defined, we also mutated the basic residues in MIP(9), a truncated form of MIP-1beta that is impaired in its ability to dimerize, to probe whether the quaternary structure of this chemokine influences its ability to bind heparin. None of the truncated variants bound as well as the full-length proteins containing the same mutation, suggesting that the MIP-1beta dimer participates in heparin binding.