Search results for " Quaternary"
showing 10 items of 148 documents
Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atom Simulations
2020
The severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic is setting the global health crisis of our time, causing a devastating societal and economic burden. An idiosyncratic trait of coronaviruses is the presence of spike glycoproteins on the viral envelope, which mediate the virus binding to specific host receptor, enabling its entry into the human cells. In spite of the high sequence identity of SARS-CoV-2 with its closely related SARS-CoV emerged in 2002, the atomic-level determinants underlining the molecular recognition of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor and, thus, the rapid virus spread into human body, remain unresolved. Here, multi-m…
Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering
2008
We demonstrate tracking of protein structural changes with time-resolved wide-angle X-ray scattering (TR-WAXS) with nanosecond time resolution. We investigated the tertiary and quaternary conformational changes of human hemoglobin under nearly physiological conditions triggered by laser-induced ligand photolysis. We also report data on optically induced tertiary relaxations of myoglobin and refolding of cytochrome c to illustrate the wide applicability of the technique. By providing insights into the structural dynamics of proteins functioning in their natural environment, TR-WAXS complements and extends results obtained with time-resolved optical spectroscopy and X-ray crystallography.
Surface and deep water conditions in the Sicily channel (central Mediterranean) at the time of sapropel S5 deposition
2011
New centennial-scale data of benthic foraminifera assemblages and of stable isotopes of foraminifera shells from the Sicily Channel, representative of surface and bottom waters, over the interval between about 140 and 110 kyr BP, are presented. During this period anoxia developed on the eastern Mediterranean basin and sapropel S5 deposited. Although anoxic sediments have not been deposited in the Sicily Channel, this area is strategic to study the character of intermediate waters, whose chemical-physical properties strongly precondition the eastern Mediterranean deep water formation. So far, no data from these water masses have been obtained, apart from the isotopic composition of shells of…
Benthic foraminifera and environmental changes in the Quaternary of the western Mediterranean coast: the core of Xeraco, Valencia, Spain
2020
The evolution of the benthic foraminiferal assemblages from a 60 m core drilled in the Quaternary lagoon of Xeraco (Valencia, Spain) is studied. Two moments of warm climate, high sea-level and maximal marine influence in the lagoon have been identified. The first one at the base of the core, punctuated by highly frequent changes during the Upper Pleistocene, and the other one in the upper end of the series during the Holocene. The presence of a middle core section with low diversity and a nearly total absence of marine foraminifers is interpreted as a regressive interval of cold climate conditions linked to a glacial stage.
A high-resolution record of the last deglaciation in the Sicily Channel based on foraminifera and calcareous nannofossil quantitative distribution
2003
Abstract Relative abundance fluctuations in planktic foraminiferal and calcareous nannofossil assemblages are reported on the basis of a high-resolution study of ODP Leg 160 Hole 963D, drilled in the Sicily Strait, near Capo Rossello (southern Sicily). With its 8 m of undisturbed sediments, the core covers the interval from 1.5 to 23 kyr, allowing a 50–100-yr sampling resolution. All the short warm and cold events and sub-events recorded in this time interval in the GRIP Greenland ice core and at several Mediterranean sites were recognized. On this basis, a total number of nine ecozones based on planktic foraminifera and seven ecozones based on calcareous nannofossils were identified. A sho…
The use of low-resolution phasing followed by phase extension from 7.6 to 2.5 Å resolution with noncrystallographic symmetry to solve the structure o…
2011
P2, the major capsid protein of bacteriophage PM2, adopts the double β-barrel fold characteristic of the PRD1-adenoviral lineage. The 2.5 Å resolution X-ray data obtained by analysis of the two major lattices of a multiple crystal of P2 were phased by molecular replacement, using as a search model structure factors to 7.6 Å resolution obtained from electron density cut from the map of the entire PM2 virion. Phase extension to 2.5 Å resolution used solely sixfold cycling averaging and solvent flattening. This represents an atypical example of an oligomeric protein for which the structure has been determined at high resolution by bootstrapping from low-resolution initial phases.
Tryptophan quenching as linear sensor for oxygen binding of arthropod hemocyanins.
2008
Oxygen binding of hemocyanins results in an absorption band around 340nm and a strong quenching of the intrinsic tryptophan fluorescence. Our study analyses in detail the fluorescence quenching within two hemocyanins, a hexamer (Panulirus interruptus) and a 4 x 6-mer (Eurypelma californicum). Based on the comparison of calculated and measured transfer efficiencies we could show that: (1) For both hemocyanins FRET (fluorescence resonance energy transfer) is exclusively responsible for quenching of the tryptophan fluorescence upon oxygen binding. (2) Tryptophan quenching by FRET is independent of the oxy- or deoxy conformation of the protein. (3) The quenching takes place at the subunit level…
Introduction of histidine residues into avidin subunit interfaces allows pH-dependent regulation of quaternary structure and biotin binding
2003
AbstractIn order to turn the subunit association and biotin binding of avidin into pH-sensitive phenomena, we have replaced individually three amino acid residues in avidin (Met96, Val115 and Ile117) with histidines in the 1–3 interface, and in combination with a histidine conversion in the 1–2 interface (Trp110). The single replacements Met96His and Val115His in the 1–3 interface were found to have a clear effect on the quaternary structure of avidin, since subunit associations of these mutants became pH-dependent. The histidine replacement in the 1–2 interface affected the biotin-binding properties of the mutants, in particular reversibility of binding and protein–ligand complex formation…
Construction of a dual chain pseudotetrameric chicken avidin by combining two circularly permuted avidins.
2004
Two distinct circularly permuted forms of chicken avidin were designed with the aim of constructing a fusion avidin containing two biotin-binding sites in one polypeptide. The old N and C termini of wild-type avidin were connected to each other via a glycine/serine-rich linker, and the new termini were introduced into two different loops. This enabled the creation of the desired fusion construct using a short linker peptide between the two different circularly permuted subunits. The circularly permuted avidins (circularly permuted avidin 5 → 4 and circularly permuted avidin 6 → 5) and their fusion, pseudotetrameric dual chain avidin, were biologically active, i.e. showed biotin binding, and…
Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS
2008
The mechanistic understanding of how membrane-embedded sensor kinases recognize signals and regulate kinase activity is currently limited. Here we report structure-function relationships of the multidomain membrane sensor kinase DcuS using solid-state NMR, structural modeling and mutagenesis. Experimental data of an individual cytoplasmic Per-Arnt-Sim (PAS) domain were compared to structural models generated in silico. These studies, together with previous NMR work on the periplasmic PAS domain, enabled structural investigations of a membrane-embedded 40-kDa construct by solid-state NMR, comprising both PAS segments and the membrane domain. Structural alterations are largely limited to prot…