Geochemistry of labile organic matter in sediments and interstitial waters of ODP Sites 107-651 and 107-653

Sediment and interstitial water from Sites 651 and 653 (ODP Leg 107) were investigated by organic geochemical methods to characterize labile organic compound classes (amino compounds and carbohydrates) and to evaluate their progressive diagenetic and thermal degradation in deep-sea sediments. Downhole distribution of dissolved organic carbon (DOC) appears related to redox zones associated with bacterial activity and of diagenetic recrystallization of biogenic tests and not so much to organic matter concentrations in ambient sediments. DOC ranges from 250 to 8300 µmol/L (3-100.1 ppm). Amino acids contribute 10%-0.3% of DOC; carbohydrates range from 78 to 5 µmol/L. Rate of degradation of amino acids by thermal effects and/or bacterial activity at both sites (significantly different in sedimentation rates: average 41 cm/1000 yr in the top 300 m at Site 651, average 3.9 cm/1000 yr in the Pliocene/Quaternary sequence at Site 653 to 220 mbsf) is more dependent on exposure time rather than on the depth within the sediment column. Variability in neutral, acidic, and basic amino acid fractions of total amino acids (with a range of 1.1-0.02 µmol/g sediment; up to 2.5% of organic carbon) varies with carbonate content and by differences in thermal stability of amino acids. Distribution patterns of monosaccharides are interpreted to result from differences in organic matter sources, sedimentation rates, and the degree of organic matter decomposition prior to and subsequent to burial. Total particulate carbohydrates range from 1.82 to 0.21 µmol/g sediment and contribute about 8% to the sedimentary organic matter. Investigation of trace metals in the interstitial waters did not show any correlation of either DOC, amino compounds, or carbohydrates.

Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone

Microcin J25 is a 21 amino acid bacterial peptide that has potent antibacterial activity against Gram-negative bacteria, resulting from its interaction with RNA polymerase. The peptide was previously proposed to have a head-to-tail cyclized peptide backbone and a tight globular structure (Blond, A., Peduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthelemy, M., Prigent, Y., Salomon, R. A., Farias, R. N., Moreno, F. & Rebuffat, S. Eur. J. Biochem. 1999, 259, 747-755). It exhibits remarkable thermal stability for a peptide of its size lacking disulfide bonds and in part this was previously proposed to derive from its macrocyclic structure. We show here that in fact the peptide does not have a head-to-tail cyclic structure but rather a side chain to backbone cyclization between Glu8 and the N-terminus. This creates an embedded ring that is threaded by the C-terminal tail of the molecule, forming a noose-like feature. The three-dimensional structure deduced from NMR data suggests that slippage of the noose is prevented by two aromatic residues flanking the embedded ring. Unthreading does not occur even when the molecule is enzymatically digested with thermolysin. The new structural interpretation fully accounts for previously reported NMR and biophysical data and is consistent with the remarkable stability of this potent antimicrobial peptide.

Twists, knots, and rings in proteins: Structural definition of the cyclotide framework

In recent years an increasing number of miniproteins containing an amide-cyclized backbone have been discovered. The cyclotide family is the largest group of such proteins and is characterized by a circular protein backbone and six conserved cysteine residues linked by disulfide bonds in a tight core of the molecule. These form a cystine knot in which an embedded ring formed by two of the disulfide bonds and the connecting backbone segment is threaded by a third disulfide bond. In the current study we have undertaken high resolution structural analysis of two prototypic cyclotides, kalata B1 and cycloviolacin O1, to define the role of the conserved residues in the sequence. We provide the first comprehensive analysis of the topological features in this unique family of proteins, namely rings (a circular backbone), twists (a cis-peptide bond in the Mobius cyclotides) and knots (a knotted arrangement of the disulfide bonds).

Solution structure of the cyclotide palicourein: Implications for the development of a pharmaceutical framework

The cyclotides are a family of disulfide-rich proteins from plants. They have the characteristic structural features of a circular protein backbone and a knotted arrangement of disulfide bonds. Structural and biochemical studies of the cyclotides suggest that their unique physiological stability can be loaned to bioactive peptide fragments for pharmaceutical and agricultural development. In particular, the cyclotides incorporate a number of solvent-exposed loops that are potentially suitable for epitope grafting applications. Here, we determine the structure of the largest known cyclotide, palicourein, which has an atypical size and composition within one of the surface-exposed loops. The structural data show that an increase in size of a palicourein loop does not perturb the core fold, to which the thermodynamic and chemical stability has been attributed. The cyclotide core fold, thus, can in principle be used as a framework for the development of useful pharmaceutical and agricultural bioactivities.