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1.
2.
Jacques Meyer 《Journal of biological inorganic chemistry》2008,13(2):157-170
An inventory of unique local protein folds around Fe–S clusters has been derived from the analysis of protein structure databases.
Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe–2S]2+,+ or [4Fe–4S]2+,+ clusters. In contrast, high-potential Fe–S clusters, notwithstanding their structural diversity, occur in only three different
protein folds. These observations suggest that the extant population of Fe–S protein folds has to a large extent been shaped
in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately
two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing
biosphere, in conditions where iron and sulfide had become poorly available, Fe–S clusters were less stable, and in addition
faced competition from heme iron and copper active sites. Among the low-potential Fe–S active sites, protein folds hosting
[4Fe–4S]2+,+ clusters outnumber those with [2Fe–2S]2+,+ ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear
clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe–S sites are evolving within
proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the
polypeptide chain. The discovery rate of novel Fe–S-containing protein folds underwent a sharp increase around 1995, and has
remained stable to this day. The current trend suggests that the mapping of the Fe–S fold space is not near completion, in
agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that
the extant structural landscape of Fe–S proteins has been shaped to a large extent by primeval geochemical conditions on one
hand, and iron–sulfur chemistry on the other. 相似文献
3.
Yutetsu Kuruma 《Origins of life and evolution of the biosphere》2007,37(4-5):409-413
Self-reproduction is one of main properties that define living cells. In order to explore the self-reproduction process for
the study of early cells, and to develop a research line somehow connected to the origin of life, we have built up a constructive
‘synthetic cells (minimal cells)’ approach. The minimal cells approach consists in the investigation of the minimal number
of elements to accomplish simple cell-like processes – like self-reproduction. Such approach belongs to the field of synthetic
biology. The minimal cells are reconstructed from a totally reconstituted cell-free protein synthesis system (PURESYSTEM)
and liposome compartments as containers. Based on this approach, we synthesized two membrane proteins (enzymes), GPAT and
LPAAT, which are involved in the phosphatidic acid biosynthesis in bacteria. Both membrane proteins were successfully synthesized
by PURESYSTEM encapsulated inside POPC liposomes. Additionally, the enzymatic activity of GPAT was restored by mixing the
expressed enzyme with lipid and by forming liposomes in situ. Through these experimental evidences, here we present a possible
model to achieve self-reproduction in minimal cells. Our results would contribute to the idea that early cells could have
been built by an extremely small number of genes.
Presented at the International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana”
Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006. 相似文献
4.
Conservation of threatened tree species requires basic information on growth rates and ages. This information is lacking for
many species, but can be obtained relatively easily from tree ring analysis. We studied four threatened Vietnamese species:
three conifers from high-elevation forests (Calocedrus macrolepis, Dacrydium elatum and Pinus
kwangtungensis) and one broad-leaved species from lowland forest (Annamocarya sinensis). We collected increment cores from remnant populations in protected areas and measured ring width. We built chronologies
and found significant correlations with rainfall (all species) and temperature (two species), indicating that rings were formed
annually. Diameter-age trajectories showed that species reached reproductive size at 60–80 years. Maximum observed ages were
128–229 years. Some species showed large variation in long-term growth rates among individuals, which was partially explained
by strong persistence of growth differences. We also assessed whether growth rates changed over time. For certain size categories
in some species, we found higher recent growth rates of juvenile trees compared to those in the distant past. This shift requires
a cautious interpretation, but is consistent with a CO2 fertilization effect. For other size categories, we found contrasting results: extant large trees had higher growth rates
as small juveniles compared to extant small trees. Such correlations, which we found for all species, suggest a ‘juvenile
selection effect’: the preferential survival of fast-growing juveniles to the canopy. Information on ages, historical growth
rates and juvenile selection effect is relevant for the planning of conservation actions. 相似文献
5.
Temporal patterns are evaluated in Neogene reef coral assemblages from the Bocas del Toro Basin of Panama in order to understand
how reef ecosystems respond to long-term environmental change. Analyses are based on a total of 1,702 zooxanthellate coral
specimens collected from six coral-bearing units ranging in age from the earliest Late Miocene to the Early Pleistocene: (1)
Valiente Formation (12–11 Ma), (2) Fish Hole Member of the Old Bank Formation (5.8–5.6 Ma), (3) La Gruta Member of the Isla
Colon Formation (2.2–1.4 Ma), (4) Ground Creek Member of the Isla Colon Formation (2.2–1.4 Ma), (5) Mimitimbi Member of the
Urracá Formation (1.2–0.8 Ma), and (6) Hill Point Member of the Urracá Formation (1.2–0.8 Ma). Over 100 coral species occur
in the six units, with faunal assemblages ranging from less than 10% extant taxa (Valiente Formation) to over 85% extant taxa
(Ground Creek Member). The collections provide new temporal constraints on the emergence of modern Caribbean reefs, with the
La Gruta Member containing the earliest occurrence of large monospecific stands of the dominant Caribbean reef coral Acropora palmata, and the Urracá Formation containing the last fossil occurrences of 15 regionally extinct taxa. Canonical correspondence
analysis of 41 Late Miocene to Recent reef coral assemblages from the Caribbean region suggests changes in community structure
coincident with effective oceanic closure of the Central American Seaway (~3.5 Ma). These changes, including increased Acropora dominance, may have contributed to a protracted period of elevated extinction debt prior to the major peak in regional coral
extinctions (~2–1 Ma). 相似文献
6.
Oxygenic photosynthetic organisms often suffer from excessive irradiance, which cause harmful effects to the chloroplast proteins
and lipids. Photoprotection and the photosystem II repair processes are the mechanisms that plants deploy to counteract the
drastic effects from irradiance stress. Although the protective and repair mechanisms seemed to be similar in most plants,
many species do confer different level of tolerance toward high light. Such diversity may originate from differences at the
molecular level, i.e., perception of the light stress, signal transduction and expression of stress responsive genes. Comprehensive
analysis of overall changes in the total pool of proteins in an organism can be performed using a proteomic approach. In this
study, we employed 2-DE/LC–MS/MS-based comparative proteomic approach to analyze total proteins of the light sensitive model
unicellular green alga Chlamydomonas reinhardtii in response to excessive irradiance. Results showed that among all the differentially expressed proteins, several heat-shock
proteins and molecular chaperones were surprisingly down-regulated after 3–6 h of high light exposure. Discussions were made
on the possible involvement of such down regulation and the light sensitive nature of this model alga. 相似文献
7.
Interactions of proteins with small molecules or other macromolecules play key roles in many biological processes and in drug
action, and NMR is an excellent tool for their structural characterization. Frequently, however, line broadening due to intermediate
exchange completely eliminates the signals needed for measuring specific intermolecular NOEs. This limits the use of NMR for
detailed structural studies in such kinetic situations. Here we show that an optimally chosen excess of ligand over protein
can reduce the extent of line broadening for both the ligand and the protein. This makes observation of ligand resonances
possible but reduces the size of the measurable NOEs due to the residual line broadening and the non-stoichiometric concentrations.
Because the solubility of small molecule drug leads are often limited to high micromolar concentrations, protein concentrations
are restricted to even lower values in the low micromolar range. At these non-stoichiometric concentrations and in the presence
of significant residual line broadening, conventional NOESY experiments very often are not sensitive enough to observe intermolecular
NOEs since the signals inverted by the NOESY preparation pulse sequence relax prior to significant NOE build up. Thus, we
employ methods related to driven NOE spectroscopy to investigate protein–ligand interactions in the intermediate exchange
regime. In this approach, individual protein resonances are selectively irradiated for up to five seconds to build up measurable
NOEs at the ligand resonances. To enable saturation of individual protein resonances we prepare deuterated protein samples
selectively protonated at a few sites so that the 1D 1H spectrum of the protein is resolved well enough to permit irradiation of individual protein signals, which do not overlap
with the ligand spectrum. This approach is suitable for measuring a sufficiently large number of protein–ligand NOEs that
allow calculation of initial complex structures, suitable for structure-based optimization of primary drug leads obtained
from high-throughput screening. The method was applied to measure individual intermolecular NOEs between the anti-apoptotic
protein Bcl-xL at 25 μM and a “first generation” small-molecule ligand, for which the spectrum is entirely broadened at stoichiometric
concentrations. This approach is general and can also be used to characterize protein–protein or protein–nucleic-acid complexes. 相似文献
8.
Previous studies from this laboratory have shown that the thermolysin fragment 121–316, comprising entirely the“all-α” COOH-terminal
structural domain 158–316, as well as fragment 206–316 (fragment FII) are able to refold into a native-like, stable structure
independently from the rest of the protein molecule. The present report describes conformational properties of fragments 228–316
and 255–316 obtained by chemical and enzymatic cleavage of fragment FII, respectively. These subfragments are able to acquire
a stable conformation of native-like characteristics, as judged by quantitative analysis of secondary structure from far-ultra-violet
circular dichroism spectra and immunochemical properties using rabbit anti-thermolysin antibodies. Melting curves of the secondary
structure of the fragments show cooperativity with a temperature of half-denaturationT
mof 65–66°C. The results of this study provide evidence that it is possible to isolate stable supersecondary structures (folding
units) of globular proteins and correlate well with predictions of subdomains of the COOH-terminal structural domain 158–316
of thermolysin. 相似文献
9.
Background
A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. 相似文献10.
We used data from the French breeding bird survey to estimate local bird species richness within sampled sites, using capture–recapture
models. We investigated the possible effects of habitat structure and composition (landscape fragmentation, habitat cover
and diversity) on estimated species richness at a local scale, and used the identified trends to help with modeling species
richness at a large spatial scale. We performed geostatistical analyses based on spatial autocorrelation – cokriging models
– to interpolate estimated species richness over the entire country, providing an opportunity to predict species-rich areas.
We further compared species richness obtained with this method to species and rarity richness obtained using a national atlas
of breeding birds. Estimated species richness was higher in species richness hotspots identified by the atlas. Combining informations
on rare species from Atlas and species richness estimates from sound sampling based schemes should help with identifying species-rich
areas for various taxa and locating biodiversity hotspots to be protected as high conservation value areas, especially in
temperate zones where diversity hotspots are likely to match centers of high species richness because of very few centers
of true endemicity. 相似文献
11.
Mattias?H?llbrink Kalle?Kilk Anna?Elmquist Pontus?Lundberg Maria?Lindgren Yang?Jiang Margus?Pooga Ursel?Soomets ülo?Langel
Cell-penetrating peptides, CPPs, are used as delivery vectors for pharmacologically interesting substances, such as antisense
oligonucleotides, proteins and peptides. We present a general principle for designing cell-penetrating peptides derived from
naturally occurring proteins as well as from randomly generated polyamino acid sequences. Thereby, we introduce a novel pharmacological
principle for identification of cell-penetrating peptides for which the applications can be numerous, including cellular transduction
vectors and mimics of intracellular protein–protein interactions. The methods of identifying a CPP comprises assessing the
averaged bulk property values of the defined sequence, and ensuring that they fall within the bulk property value interval
obtained from the training set. Despite this simplistic approach, the search criteria proved useful for finding CPP properties
in either proteins or random sequences. We have experimentally verified cell-penetrating properties of 10–20-mer peptides
derived from naturally occurring proteins as well as from random poly-amino acids. We note that since CPPs can be found in
part of the protein sequences that may govern protein interactions, it is possible to produce cell-penetrating protein agonists
or antagonists. 相似文献
12.
Forests soils should be neither sinks nor sources of carbon in a long-term perspective. From a Swedish perspective the time
since the last glaciation has probably not been long enough to reach a steady state, although changes are currently very slow.
In a shorter perspective, climatic and management changes over the past 100 years have probably created imbalances between
litter input to soils and organic carbon mineralisation. Using extant data on forest inventories, we applied models to analyse
possible changes in the carbon stocks of Swedish forest soils. The models use tree stocks to provide estimates of tree litter
production, which are fed to models of litter decomposition and from which carbon stocks are calculated. National soil carbon
stocks were estimated to have increased by 3 Tg yr−1 or 12–13 g m−2 yr−1 in the period 1926–2000 and this increase will continue because soil stocks are far from equilibrium with current litter
inputs. The figure obtained is likely to be an underestimation because wet sites store more carbon than predicted here and
the inhibitory effect of nitrogen deposition on soil carbon mineralisation was neglected. Knowledge about site history prior
to the calculation period determines the accuracy of current soil carbon stocks estimates, although changes can be more accurately
estimated. 相似文献
13.
Forests soils should be neither sinks nor sources of carbon in a long-term perspective. From a Swedish perspective the time
since the last glaciation has probably not been long enough to reach a steady state, although changes are currently very slow.
In a shorter perspective, climatic and management changes over the past 100 years have probably created imbalances between
litter input to soils and organic carbon mineralisation. Using extant data on forest inventories, we applied models to analyse
possible changes in the carbon stocks of Swedish forest soils. The models use tree stocks to provide estimates of tree litter
production, which are fed to models of litter decomposition and from which carbon stocks are calculated. National soil carbon
stocks were estimated to have increased by 3 Tg yr−1 or 12–13 g m−2 yr−1 in the period 1926–2000 and this increase will continue because soil stocks are far from equilibrium with current litter
inputs. The figure obtained is likely to be an underestimation because wet sites store more carbon than predicted here and
the inhibitory effect of nitrogen deposition on soil carbon mineralisation was neglected. Knowledge about site history prior
to the calculation period determines the accuracy of current soil carbon stocks estimates, although changes can be more accurately
estimated.
This article has previously been published in issue 82/3, under DOI . 相似文献
14.
Deborah L. Rogers A. Colin Matheson J. Jesùs Vargas-Hernández Jesús J. Guerra-Santos 《Biodiversity and Conservation》2006,15(2):779-798
Monterey pine (Pinus radiata D. Don) has only five extant native populations: three disjunct populations along the coast of California, USA and two on
Mexican islands. All populations have been influenced by human activity, but the island populations in particular have been
affected by introduced biota. On Guadalupe Island, the pine population has suffered drastically from overgrazing by introduced
goats. We visited both island populations and described their status, took measurements, and made seed collections. We counted
approximately 200 mature pine trees and virtually no seedlings on Guadalupe Island: a reduction of approximately half the
population in the last 50 years. The trees are all large (mean diameter of 144 cm) –considerably larger than trees from the
other four populations – and arguably near the end of their natural lifespan. The population on Cedros Island is much more
robust, with thousands of trees. None sampled were as large as those on Guadalupe Island (mean diameter of 20 cm) and many
groves were young and even-aged – presumably the consequence of natural regeneration after a recent fire. Tissue samples from
trees on both islands did not show evidence of infection from the pitch canker pathogen, Fusarium circinatum, that has caused significant mortality in the three mainland populations. Caution is recommended in any restoration activity
for the Guadalupe Island pines. Inbreeding levels could indicate the need for some planting or seeding intervention but there
are also risks associated with this. Natural regeneration – after goat removal – is preferred. 相似文献
15.
Carbonaro M 《Amino acids》2006,31(4):485-488
Summary. Two-dimensional electrophoresis (2-DE) was used for tracing in vivo gastrointestinal digestion of milk proteins in a rapid
model system with rats. Contents of stomach and small intestine from digestion trials with rats given a single dose of milk
powder were recovered after 1 hour. They were then subjected to 2-DE (IEF and SDS-PAGE). 2-DE showed undigested proteins in
a MW range 13.0–66.0 kDa in stomach and 13.0–25.0 kDa in the small intestine, thus indicating that milk proteins are slowly
digested. This approach may shed light on pattern of protein digestion and mechanism of amino acid and peptide assimilation. 相似文献
16.
Tonelli M Singarapu KK Makino S Sahu SC Matsubara Y Endo Y Kainosho M Markley JL 《Journal of biomolecular NMR》2011,51(4):467-476
Perdeuteration, selective deuteration, and stereo array isotope labeling (SAIL) are valuable strategies for NMR studies of
larger proteins and membrane proteins. To minimize scrambling of the label, it is best to use cell-free methods to prepare
selectively labeled proteins. However, when proteins are prepared from deuterated amino acids by cell-free translation in
H2O, exchange reactions can lead to contamination of 2H sites by 1H from the solvent. Examination of a sample of SAIL-chlorella ubiquitin prepared by Escherichia coli cell-free synthesis revealed that exchange had occurred at several residues (mainly at Gly, Ala, Asp, Asn, Glu, and Gln).
We present results from a study aimed at identifying the exchanging sites and level of exchange and at testing a strategy
for minimizing 1H contamination during wheat germ cell-free translation of proteins produced from deuterated amino acids by adding known inhibitors
of transaminases (1 mM aminooxyacetic acid) and glutamate synthetase (0.1 mM l-methionine sulfoximine). By using a wheat germ cell-free expression system, we produced [U–2H, 15N]-chlorella ubiquitin without and with added inhibitors, and [U–15N]-chlorella ubiquitin as a reference to determine the extent of deuterium incorporation. We also prepared a sample of [U–13C, 15N]-chlorella ubiquitin, for use in assigning the sites of exchange. The added inhibitors did not reduce the protein yield
and were successful in blocking hydrogen exchange at Cα sites, with the exception of Gly, and at Cβ sites of Ala. We discovered, in addition, that partial exchange occurred with or without the inhibitors at certain side-chain
methyl and methylene groups: Asn–Hβ, Asp–Hβ, Gln–Hγ, Glu–Hγ, and Lys–Hε. The side-chain labeling pattern, in particular the mixed chiral labeling resulting from partial exchange at certain sites,
should be of interest in studies of large proteins, protein complexes, and membrane proteins. 相似文献
17.
Susan Cachel 《Primates; journal of primatology》1983,24(1):109-117
Diets of the Oligocene anthropoidsAegyptopithecus zeuxis andApidium phiomense are inferred from measurements of the anterior and posterior dentition of these species. Ideas are presented which can be
checked as the hypodigms expand. Comparisons with extant anthropoids demonstrate a probably frugivorous diet forA. zeuxis, while the diet ofA. phiomense was not characterized by a high degree of frugivory requiring extensive incisal preparation of food. Additional inferences
about the diet ofA. phiomense might be gleaned from future examination of incisor morphology, implantation and occlusion. Even when allowance is made for
the presence of P2 inA. phiomense, the dietary position of this species with respect to extant anthropoids is equivocal, and it is possible that the normal
anthropoid relationship between anterior and posterior dentitions, with a small incisor span correlating with a great amount
of mastication, had yet to be developed.
This report is based in part on an invited paper “Function in primate masticatory musculature as demonstrated by muscle weights”
delivered at the symposium “The Behavioral and Morphological Adaptations to Diet Among Primates,” 46th Annual Meeting, American
Association of Physical Anthropologists, Seattle, Washington, April 13–16, 1977. 相似文献
18.
Outi Heikkinen Perttu Permi Harri Koskela Jari Ylänne Ilkka Kilpeläinen 《Biomolecular NMR assignments》2009,3(1):53-56
Filamins are large actin-binding and cross-linking proteins which act as linkers between the cytoskeleton and various signaling
proteins. Filamin A (FLNa) is the most abundant of the three filamin isoforms found in humans. FLNa contains an N-terminal
actin-binding domain and 24 immunoglobulin-like (Ig) domains. The Ig domains are responsible for the FLNa dimerization and
most of the interactions that FLNa has with numerous other proteins. There are several crystal and solution structures from
isolated single Ig domains of filamins in the PDB database, but only few from longer constructs. Here, we present nearly complete
chemical shift assignments of FLNa tandem Ig domains 16–17 and 18–19. Chemical shift mapping between FLNa tandem Ig domain
16–17 and isolated domain 17 suggests a novel domain–domain interaction mode. 相似文献
19.
C. Stathopoulos G. Georgiou C. F. Earhart 《Applied microbiology and biotechnology》1996,45(1-2):112-119
The Lpp′OmpA(46–159) hybrid protein can serve as an efficient targeting vehicle for localizing a variety of procaryotic and
eucaryotic soluble proteins onto the E. coli surface, thus providing a system for several possible biotechnology applications. Here we show that fusions between Lpp′OmpA(46–159)
and bacterial alkaline phosphatase (PhoA), a normally periplasmic dimeric enzyme, are also targeted to the outer membrane.
However, protease accessibility experiments and immunoelectron microscopy revealed that, unlike other periplasmic proteins,
the PhoA domain of these fusions is not exposed on the cell surface in cells having an intact outer membrane. Conditions that
affect the formation of disulfide bonds and the folding of the PhoA domain in the periplasm not only did not facilitate targeting
to the cell surface but led to lethality when the fusion was expressed from a high-copy-number plasmid. Furthermore, E. coli expressing the Lpp′OmpA(46–159)-PhoA fusion exhibited strain- and temperature-dependent alterations in outer-membrane permeability.
Our results are consistent with previous studies with other vehicles indicating that PhoA is not displayed on the surface
when fused to cell-surface expression vectors. Presumably, the enzyme rapidly assumes a tightly folded dimeric conformation
that cannot be transported across the outer membrane. The large size and quaternary structure of PhoA may define a limitation
of the Lpp′OmpA(46– 159) fusion system for the display of periplasmic proteins on the cell surface. Alkaline phosphatase is
a unique protein among a group of five periplasmic proteins (β-lactamase, alkaline phosphatase, Cex cellulase, Cex cellulose-binding
domain, and a single-chain Fv antibody fragment), which have been tested as passengers for the Lpp′OmpA(46–159) expression
system to date, since it was the only protein not displayed on the surface.
Received: 23 March 1995/Received revision: 29 July 1995/Accepted: 22 August 1995 相似文献
20.
14-3-3 proteins are conserved regulatory proteins present in all eukaryotic cells that control numerous cellular activities
via targeted protein interactions. To elucidate the interaction between P14-3-3 from Physarum polycephalum and actin in living cells, PCR and DNA recombination were used to generate various P14-3-3 and actin constructs. Yeast two-hybrid
assay and FRET were employed to characterize the interaction between P14-3-3 and actin. The two-hybrid assay indicated that
P14-3-3 N-terminal 76–108 amino acids and the C-terminal 207–216 amino acids played an important role in mediating interactions
with actin, and the actin N-terminal 1–54 amino acids and the C-terminal 326–376 amino acids are also crucial in the interactions
with the mPa, a P14-3-3 with mutations at Ser62 (Ser62 → Gly62). Mutations to potential phosphorylation sites did not affect
interactions between P14-3-3 and actin. FRET results demonstrated that P14-3-3 co-localized with actin with a FRET efficiency
of 22.2% and a distance of 7.4 nm and that P14-3-3 N-terminal 76–108 and C-terminal 207–216 amino acids were important in
mediating this interaction, the truncated actin peptides without either the N-terminal 1–54 or C-terminal 326–376 amino acids
interacted with P14-3-3, consistent with the results obtained from the yeast two-hybrid assay. Based on data obtained, we
identified critical actin and P14-3-3 contact regions. 相似文献