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At least 163 records · Page 9Linked to original sources
PubMed2004

Acid denaturation and refolding of green fluorescent protein.

Green fluorescent protein from the jellyfish Aequorea victoria can serve as a good model protein to understand protein folding in a complex environment with molecular chaperones and other macromolecules such as those in biological cells, but little is known about the detailed mechanisms of the in vitro folding of green fluorescent protein itself. We therefore investigated the kinetic refolding of a mutant (F99S/M153T/V163A) of green fluorescent protein, which is known to mature more efficiently than the wild-type protein, from the acid-denatured state; refolding was observed by chromophore fluorescence, tryptophan fluorescence, and far-UV CD, using a stopped-flow technique. In this study, we demonstrated that the kinetics of the refolding of the mutant have at least five kinetic phases and involve nonspecific collapse within the dead time of a stopped-flow apparatus and the subsequent formation of an on-pathway intermediate with the characteristics of the molten globule state. We also demonstrated that the slowest phase and a major portion of the second slowest phase were rate-limited by slow prolyl isomerization in the intermediate state, and this rate limitation accounts for a major portion of the observed kinetics in the folding of green fluorescent protein.

Animals↗
PubMed2005

Oxidative chemistry in the GFP active site leads to covalent cross-linking of a modified leucine side chain with a histidine imidazole: implications for the mechanism of chromophore formation.

The mechanism of chromophore biosynthesis in green fluorescent protein (GFP) is triggered by a spontaneous main chain cyclization reaction of residues 65-67. Here, we demonstrate that the initially colorless Y66L variant, designed to trap chromophore precursor states, is oxidatively modified to generate yellow chromophores that absorb at 412 and 374 nm. High- and low-pH crystal structures determined to 2.0 and 1.5 A resolution, respectively, are consistent with pi-orbital conjugation of a planar Leu66-derived adduct with the imidazolinone ring, which is approximately 90 and 100% dehydrated, respectively. Time-, base-, and oxygen-dependent optical properties suggest that the yellow chromophores are generated from a 338 nm-absorbing intermediate, interpreted to be the Y66L analogue of the wild-type GFP chromophore. Generation of this species is catalyzed by a general base such as formate, and proceeds via a cyclization-oxidation-dehydration mechanism. The data suggest that a hydration-dehydration equilibrium exists in the cyclic form of the peptide, and that dehydration is favored upon extensive conjugation with the modified side chain. We conclude that the mechanism of GFP chromophore biosynthesis is not driven by the aromatic character of residue 66. In the low-pH X-ray structure, a highly unusual cross-link is observed between His148 and the oxidized Leu66 side chain, suggesting a conjugate addition reaction of the imidazole nitrogen to the highly electrophilic diene group of the yellow chromophore. The reactivity described here further expands the chemical diversity observed in the active site of GFP-like proteins, and may allow for covalent attachment of functional groups to the protein scaffold for catalytic purposes.

Amino Acid Substitution↗
PubMed2005

Development and characterization of green fluorescent protein mutants with altered lifetimes.

Multiple-probe fluorescence imaging applications demand an ever-increasing number of resolvable probes, and the use of fluorophores with resolvable fluorescence lifetimes can help meet this demand. Green fluorescent protein (GFP) and its variants have been widely used in spectrally resolved multiprobe imaging, but as yet, there has not been a systematic set of mutants generated with resolvable lifetimes. Therefore, to generate such mutants, we have utilized error-prone PCR and fluorescence lifetime imaging to screen for mutants of UV-excited green fluorescent protein (GFPuv) that exhibit altered fluorescence decay lifetimes. This has resulted in the isolation of GFPuv mutants displaying at least three distinctly different lifetimes in the range of 1.9-2.8 ns. Mutation of Y145 to either histidine or cysteine was found to shift the fluorescence lifetime of GFPuv from 3.03 +/- 0.03 to 2.78 +/- 0.05 ns for the Y145H mutant and to 2.74 +/- 0.05 ns for Y145C. Some of the shorter-lifetime mutants exhibited excitation peaks that were red-shifted relative to their maximal absorption, indicating that the mutations allowed the adoption of additional conformations relative to wtGFPuv. The utility of these mutants for applications in simultaneous imaging and quantification is shown by the ability to quantify the composition of binary mixtures in time-resolved images using a single detector channel. The application of the screening method for generating lifetime mutants of other fluorescent proteins is also discussed.

Animals↗
PubMed2005

4-Hydroxybenzoyl derivative from the aqueous extract of the hydroid Campanularia sp.

A new compound, N-(4-guanidinobutyl)-2-(4-hydroxyphenyl)-2-oxo-acetamide (1) was isolated from the aqueous extract of the hydroid Campanularia sp. Its structure was elucidated using NMR spectroscopic techniques and mass spectrometric analysis. The most stable conformation was determined using molecular modeling and the results of a NOESY experiment. Although compound 1 shows structural similarities to some highly potent histone deacetylase inhibitors (HDACi), e.g., suberoylanilide hydroxamic acid (SAHA) (2) and trichostatin A (TSA) (3), it does not inhibit the growth of ARP-1 cells at 100 microM concentration, a significant indication that it has no inhibitory activity to HDACs.

Animals↗
PubMed2002

Evolutionary conservation of the chromatin modulator Polycomb in the jellyfish Podocoryne carnea.

Polycomb-group (PcG) proteins form chromatin-associated multimeric complexes, which are responsible for the maintenance of the transcriptionally repressive state of regulatory genes during development. We have isolated a Polycomb homologue of the hydrozoan Podocoryne carnea by a PCR-based approach. Our results demonstrate that structure and function of Polycomb-group proteins have been conserved in evolution from cnidarians to vertebrates since Podocoryne Polycomb interacts in yeast with mouse dinG/RING1B, an interaction partner of the mouse Polycomb homologue MPc3. Polycomb is expressed throughout the life cycle of Podocoryne. In situ hybridization reveals a differential expression pattern in proliferating and differentiating tissues of the developing medusa bud. In the transdifferentiation of activated isolated striated muscle of the medusa to smooth muscle and RFamide-positive nerve cells, Polycomb expression is strongly increased when differentiation into nerve cells occurs.

Amino Acid Sequence↗
PubMedDate not supplied

Complication of a Portuguese man-of-war envenomation to the foot: a case report.

Jellyfish stings have become more prevalent on account of larger commercial presence along coastal waterways. Stings are referred to as envenomations, due to the process of a neurotoxic venom being injected into the victim at the site of the sting. These events are usually mild, and for the most part, confined to local hypersensitivity reactions at the site of the injury. Certain species of jellyfish, however, have been associated with more severe, systemic insults including muscle cramping, respiratory distress, hypotension, circulatory collapse and death. One such example of a more potent venom is the Portuguese man-of-war. Most case reports of Portuguese man-of-war envenomations do not involve local soft tissue necrosis. The purpose of this case report is to present such a consequence after a jellyfish sting to the dorsum of the foot. A large area of skin necrosis developed after an envenomation that required extensive debridement and skin grafting.

Adult↗
PubMed2003

Nonlinear oscillations in marine hydroids.

Irregular oscillations in a colony of marine hydroids Podocoryne carnea were investigated. Quantitative characteristics were obtained as a result of long term (10-12 h) monitoring of oscillations at arbitrary sites. The sliding window spectra as well as the pulse-to-pulse dynamics argue the transient chaotic behavior of hydroid colony. The significant change of amplitudes and frequencies in intact colony oscillations after feeding and long sustained oscillations of stolons separated from colony suggest that the irregular activity could be determined by the network of pacemakers residing in stolon wall cells. These are influenced mechanically by the amount of digesting food and/or by chemical action of nutrients inside the stolon lumen. The possible correlation of these oscillations which can evoke Ca(2+) waves in stolon wall cells is discussed.

Animals↗
PubMed2003

A Geometro-mechanical model for pulsatile morphogenesis.

A model is proposed which imitates the morphogenesis of several species of the lower invertebrate animals, the hydroid polyps and permits the derivation of the geometry (surface curvature) of each developmental stage from that of the preceding stage. The model is based upon two experimentally verified assumptions. First, neighbouring cells are assumed to compress each other laterally in a regular and species-specific pulsatile manner. It is this pressure, and/or an active cell reaction to it, which changes the curvature of a cell layer. Secondly, cell layers are assumed to have quasi-elastic properties tending to smooth out their curvature. With our model, the different pulsatile patterns of cell-cell pressure are reproduced and the elasticity parameters are modulated. As a result, within a large zone of parameter values (a so-called "morphogenetic zone", MZ) realistic shapes of the rudiments are reproduced. The main principles of the model can also be used for interpreting the morphogenesis of other groups of animals. A suggested model emphasizes the self-organizing properties of a "stressed geometry" of embryonic rudiments.

Cell Size↗
PubMed2004

GFP-like proteins as ubiquitous metazoan superfamily: evolution of functional features and structural complexity.

Homologs of the green fluorescent protein (GFP), including the recently described GFP-like domains of certain extracellular matrix proteins in Bilaterian organisms, are remarkably similar at the protein structure level, yet they often perform totally unrelated functions, thereby warranting recognition as a superfamily. Here we describe diverse GFP-like proteins from previously undersampled and completely new sources, including hydromedusae and planktonic Copepoda. In hydromedusae, yellow and nonfluorescent purple proteins were found in addition to greens. Notably, the new yellow protein seems to follow exactly the same structural solution to achieving the yellow color of fluorescence as YFP, an engineered yellow-emitting mutant variant of GFP. The addition of these new sequences made it possible to resolve deep-level phylogenetic relationships within the superfamily. Fluorescence (most likely green) must have already existed in the common ancestor of Cnidaria and Bilateria, and therefore GFP-like proteins may be responsible for fluorescence and/or coloration in virtually any animal. At least 15 color diversification events can be inferred following the maximum parsimony principle in Cnidaria. Origination of red fluorescence and nonfluorescent purple-blue colors on several independent occasions provides a remarkable example of convergent evolution of complex features at the molecular level.

Animals↗