Analysis of membrane and surface protein sequences with the hydrophobic moment plot.

Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.

/pdf/the-genome-of-the-kinetoplastid-parasite-leishmania-major-1snhp975lu.pdf

The genome of the kinetoplastid parasite, Leishmania major.

Nerve terminals are specific sites of action of a very large number of toxins produced by many different organisms. The mechanism of action of three groups of presynaptic neurotoxins that interfere directly with the process of neurotransmitter release is reviewed, whereas presynaptic neurotoxins acting on ion channels are not dealt with here. These neurotoxins can be grouped in three large families: 1) the clostridial neurotoxins that act inside nerves and block neurotransmitter release via their metalloproteolytic activity directed specifically on SNARE proteins; 2) the snake presynaptic neurotoxins with phospholipase A(2) activity, whose site of action is still undefined and which induce the release of acethylcholine followed by impairment of synaptic functions; and 3) the excitatory latrotoxin-like neurotoxins that induce a massive release of neurotransmitter at peripheral and central synapses. Their modes of binding, sites of action, and biochemical activities are discussed in relation to the symptoms of the diseases they cause. The use of these toxins in cell biology and neuroscience is considered as well as the therapeutic utilization of the botulinum neurotoxins in human diseases characterized by hyperfunction of cholinergic terminals.

https://www.physiology.org/doi/pdf/10.1152/physrev.2000.80.2.717

Neurotoxins Affecting Neuroexocytosis

Publisher Summary This chapter describes the present state of the studies of the molten globule state and its role in protein folding and physiological processes Recent data on the intermediates (equilibrium and kinetic), focusing attention on the molten globule state are discussed in the chapter The molten globule has a native-like overall architecture (folding pattern) without including the rigid packing of side chains It is separated by first-order phase transitions from both the native and the unfolded states and represents a third thermodynamic state of protein molecules It is a universal kinetic intermediate in protein folding; the structure of this intermediate is similar to the structure of the equilibrium molten globule It is predicted and confirmed experimentally that the molten globule state can exist in a living cell and plays an important role in a number of physiological processes

Molten globule and protein folding.

The spatial distribution of the hydrophobic side chains in globular proteins is of considerable interest. It was recognized previously1 that most of the α-helices of myoglobin and haemoglobin are amphiphilic; that is, one surface of each helix projects mainly hydrophilic side chains, while the opposite surface projects mainly hydrophobic side chains. To quantify the amphiphilicity of a helix, here we define the mean helical hydrophobic moment, 〈μH〉 = |ΣNi=1 H⇀i/N, to be the mean vector sum of the hydrophobicities H⇀i of the side chains of a helix of N residues. The length of a vector H⇀i is the signed numerical hydrophobicity associated with the type of side chain, and its direction is determined by the orientation of the side chain about the helix axis. A large value of 〈μH〉 means that the helix is amphiphilic perpendicular to its axis. We have classified α-helices by plotting their mean helical moment versus the mean hydrophobicity of their residues, and report that trans-membrane helices, helices from globular proteins and helices which are believed to seek surfaces between aqueous and non-polar phases, cluster in different regions of such a plot. We suggest that this classification may be useful in identifying helical regions of proteins which bind to the surface of biological membranes. The concept of the hydrophobia moment can be generalized also to non-helical protein structures.

The helical hydrophobic moment: a measure of the amphiphilicity of a helix

Secondary structure of diphtheria toxin and its fragments interacting with acidic liposomes studied by polarized infrared spectroscopy.

Two different lipid-associating domains have been identified in the B fragment of diphtheria toxin using automated Edman degradation of its cyanogen bromide peptides, secondary structure prediction analysis, and comparisons with known phospholipid-interacting proteins. The first domain is located in the highly hydrophilic (polarity index [PI] = 61.0%) 9.00-dalton N-terminal region of fragment B. This region shows primary and predicted secondary structures dramatically similar to those found for the phospholipid headgroup-binding domains of human apolipoprotein A1 (surface lipid-associating domain). The second domain is located in the highly hydrophobic (PI = 32.4%) middle region of fragment B. Its structure resembles that found for the membranous domain of intrinsic membrane proteins (transverse lipid-associating domain). In contrast, the hydrophilic C-terminal 8,000-dalton region of fragment B (PI = 53.8%) does not show structural similarity with lipid-associating domains.

https://rupress.org/jcb/article-pdf/87/3/837/1389193/837.pdf

Primary structure of diphtheria toxin fragment B: structural similarities with lipid-binding domains.

Most lung disorders are known to be associated to considerable modifications of surfactant composition Numerous of these abnormalities have been exploited in the past to diagnose lung diseases, allowing proper treatment and follow-up Diagnosis was then based on phospholipid content, surface tension and cytological features of the epithelial lining fluid (ELF), sampled by bronchoalveolar lavage (BAL) during fiberoscopic bronchoscopy Today, it appears that the protein content of ELF displays a remarkably high complexity, not only due to the wide variety of the proteins it contains but also because of the great diversity of their cellular origins The significance of the use of proteome analysis of BAL fluid for the search for new lung disease marker proteins and for their simultaneous display and analysis in patients suffering from lung disorders has been examined

/pdf/proteomics-as-the-tool-to-search-for-lung-disease-markers-in-nz4k8qk4s4.pdf

Proteomics as the tool to search for lung disease markers in bronchoalveolar lavage

Clara cell protein is a 16-17 kDa protein (CC16) secreted by Clara cells in the bronchiolar lining fluid of the lung. In order to investigate the potential of this protein as a pulmonary marker in animals, CC16 was isolated from rat bronchoalveolar lavage fluid (BALF) and a sensitive latex immunoassay applicable to both rat and mouse CC16 was developed. The pattern of CC16 concentrations in rat biological fluids determined by the immunoassay was consistent with the hypothesis of a passive diffusion of the protein across the bronchoalveolar/blood barriers showing a difference of more than 5,000 fold between the concentration in the epithelial lining fluid (mean, 140 mg x L(-1)) and that in serum (20 microg x L(-1)) or urine (3 microg x L(-1)). In BALF, the CC16 concentration averaged 5,500 microg x L(-1) and was of the same magnitude as that determined on lung and trachea homogenates. CC16 was also detectable in amniotic fluid with a mean value of 800 microg x L(-1) before delivery. Damage of Clara cells produced by methylcyclopentadienyl manganese tricarbonyl resulted in a significant decrease of CC16 in BALF but did not affect the serum levels of the protein. The nephrotoxicant sodium chromate by contrast had no influence on the CC16 content of BALF but markedly increased CC16 levels in both serum and urine as a result of impaired glomerular filtration and tubular reabsorption, respectively. In conclusion, mouse or rat Clara cell protein of 16-17 kDa can easily be quantified, not only in bronchoalveolar lavage fluid, but also in extrapulmonary fluids such as serum or urine. Thus, in rodents, Clara cell protein of 16-17 kDa follows the same metabolic pathway as in humans, diffusing from the respiratory tract into serum where it is eliminated by the kidneys. This serum Clara cell protein of 16-17 kDa may be useful as a peripheral marker of events taking place in the respiratory tract.

https://erj.ersjournals.com/content/erj/11/3/726.full.pdf

Quantification of Clara cell protein in rat and mouse biological fluids using a sensitive immunoassay

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2883%2980941-7

Paul Falmagne

Papers

Secondary structure of diphtheria toxin and its fragments interacting with acidic liposomes studied by polarized infrared spectroscopy.

Primary structure of diphtheria toxin fragment B: structural similarities with lipid-binding domains.

Proteomics as the tool to search for lung disease markers in bronchoalveolar lavage

Quantification of Clara cell protein in rat and mouse biological fluids using a sensitive immunoassay

Localization in diphtheria toxin fragment B of a region that induces pore formation in planar lipid bilayers at low pH.