Biomedical subjects

Jennifer S Martinez

Publications and source records attributed to Jennifer S Martinez.

4 recordsLinked to original sources

PubMed2006

Antibody binding loop insertions as diversity elements.

In the use of non-antibody proteins as affinity reagents, diversity has generally been derived from oligonucleotide-encoded random amino acids. Although specific binders of high-affinity have been selected from such libraries, random oligonucleotides often encode stop codons and amino acid combinations that affect protein folding. Recently it has been shown that specific antibody binding loops grafted into heterologous proteins can confer the specific antibody binding activity to the created chimeric protein. In this paper, we examine the use of such antibody binding loops as diversity elements. We first show that we are able to graft a lysozyme-binding antibody loop into green fluorescent protein (GFP), creating a fluorescent protein with lysozyme-binding activity. Subsequently we have developed a PCR method to harvest random binding loops from antibodies and insert them at predefined sites in any protein, using GFP as an example. The majority of such GFP chimeras remain fluorescent, indicating that binding loops do not disrupt folding. This method can be adapted to the creation of other nucleic acid libraries where diversity is flanked by regions of relative sequence conservation, and its availability sets the stage for the use of antibody loop libraries as diversity elements for selection experiments.

Antibody Diversity↗

PubMed2005

Micelle-to-vesicle transition of an iron-chelating microbial surfactant, marinobactin E.

Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) techniques have been applied to study the self-assembly processes of a microbially produced siderophore, marinobactin E (ME). ME is one of a series of marinobactins A-E that facilitate Fe(III) acquisition by the source bacterium through coordination of Fe(III) by the marinobactin headgroup. ME is a six-amino-acid peptide amphiphile appended by palmitic acid (C16), and differs only in the nature of the fatty acid moiety from the other marinobactins. Apo-ME (uncoordinated ME) assembles to form micelles with an average diameter of 4.0 nm. Upon coordination of one equivalent of Fe(III), the mean micellar diameter of Fe(III)-ME shrinks to approximately 2.8 nm. However, in the presence of excess Fe(III), Fe(III)-ME undergoes a micelle-to-vesicle transition (MVT). At a small excess of Fe(III) over Fe(III)-ME (i.e., <1.2 Fe(III)/ME), a fraction of the Fe(III)-ME micelles rearrange into approximately 200 nm diameter unilamellar vesicles. At even greater Fe(III)/ME ratios (e.g., 2-3) multilamellar aggregates begin to emerge, consistent with either multilamellar vesicles or lamellar stacks. The MVT exhibited by ME may represent a unique mechanism by which marine bacteria may detect and sequester iron required for growth.

Iron Chelating Agents↗

PubMed2003

Structure and membrane affinity of a suite of amphiphilic siderophores produced by a marine bacterium.

Iron concentrations in the ocean are low enough to limit the growth of marine microorganisms, which raises questions about the molecular mechanisms these organisms use to acquire iron. Marine bacteria have been shown to produce siderophores to facilitate iron(III) uptake. We describe the structures of a suite of amphiphilic siderophores, named the amphibactins, which are produced by a nearshore isolate, gamma Proteobacterium, Vibrio sp. R-10. Each amphibactin has the same Tris-hydroxamate-containing peptidic headgroup composed of three ornithine residues and one serine residue but differs in the acyl appendage, which ranges from C-14 to C-18 and varies in the degree of saturation and hydroxylation. Although amphiphilic siderophores are relatively rare, cell-associated amphiphilic siderophores are even less common. We find that the amphibactins are cell-associated siderophores. As a result of the variation in the nature of the fatty acid appendage and the cellular location of the amphibactins, the membrane partitioning of these siderophores was investigated. The physiological mixture of amphibactins had a range of membrane affinities (3.8 x 10(3) to 8.3 x 10(2) M(-1)) that are larger overall than other amphiphilic siderophores, likely accounting for their cell association. This cell association is likely an important defense against siderophore diffusion in the oceanic environment. The phylogenetic affiliation of Vibrio sp. R-10 is discussed, as well as the observed predominance of amphiphilic siderophores produced by marine bacteria in contrast to those produced by terrestrial bacteria.

Bacteria↗

PubMed2002

Membrane affinity of the amphiphilic marinobactin siderophores.

Marinobactins are a class of newly discovered marine bacterial siderophores with a unique amphiphilic structure, suggesting that their functions relate to interactions with cell membranes. Here we use small and large unilamellar L-alpha-dimyristoylphosphatidylcholine vesicles (SUVs and LUVs) as model membranes to examine the thermodynamics and kinetics of the membrane binding of marinobactins, particularly marinobactin E (apo-M(E)) and its iron(III) complex, Fe-M(E). Siderophore-membrane interactions are characterized by NMR line broadening, stopped-flow spectrophotometry, fluorescence quenching, and ultracentrifugation. It is determined that apo-M(E) has a strong affinity for lipid membranes with molar fraction partition coefficients K(x)()(apo)(-)(M)E = 6.3 x 10(5) for SUVs and 3.6 x 10(5) for LUVs. This membrane association is shown to cause only a 2-fold decrease in the rate of iron(III) binding by apo-M(E). However, upon the formation of the iron(III) complex Fe-M(E), the membrane affinity of the siderophore decreased substantially (K(x)()(Fe)(-)(M)E = 1.3 x 10(4) for SUVs and 9.6 x 10(3) for LUVs). The kinetics of membrane binding and dissociation by Fe-M(E) were also determined (k(on)(Fe)(-)(M)E = 1.01 M(-)(1) s(-)(1); k(off)(Fe)(-)(M)E = 4.4 x 10(-)(3) s(-)(1)). The suite of marinobactins with different fatty acid chain lengths and degrees of chain unsaturation showed a range of membrane affinities (5.8 x 10(3) to 36 M(-)(1)). The affinity that marinobactins exhibit for membranes and the changes observed upon iron binding could provide unique biological advantages in a receptor-assisted iron acquisition process in which loss of the iron-free siderophore by diffusion is limited by the strong association with the lipid phase.

Cell Membrane↗