3,001 research outputs found
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding
No full textRecent work has shown that the nature of hydration of pure hydrophobic surfaces changes with the length scale considered: water hydrogen-bonding networks adapt to small exposed hydrophobic species, hydrating or ‘‘wetting’’ them at relatively high
densities, whereas larger hydrophobic areas are ‘‘dewetted’’
[Chandler D (2005), Nature 29:640 – 647]. Here we determine whether this effect is also present in peptides by examining the
folding of a beta-hairpin (the 14-residue amyloidogenic prion protein
H1 peptide), using microsecond time-scale molecular dynamics
simulations. Two simulation models are compared, one explicitly
including the water molecules, which may thus adapt locally to
peptide configurations, and the other using a popular continuum
approximation, the generalized Born/surface area implicit solvent
model. The results obtained show that, in explicit solvent, peptide
conformers with high solvent-accessible hydrophobic surface area
indeed also have low hydration density around hydrophobic residues, whereas a concomitant higher hydration density around
hydrophilic residues is observed. This dewetting effect stabilizes
the fully folded beta-hairpin state found experimentally. In contrast,
the implicit solvent model destabilizes the fully folded hairpin, tending to cluster hydrophobic residues regardless of the size of
the exposed hydrophobic surface. Furthermore, the rate of the
conformational transitions in the implicit solvent simulation is
almost doubled with respect to that of the explicit solvent. The
results suggest that dehydration-driven solvent exposure of hydrophobic surfaces may be a significant factor determining peptide
conformational equilibria
A generalized born implicit-membrane representation compared to experimental insertion free energies.
No full textAn implicit-membrane representation based on the generalized Born theory of solvation has been developed. The method was parameterized against the water-to-cyclohexane insertion free energies of hydrophobic side-chain analogs. Subsequently, the membrane was compared with experimental data from translocon inserted polypeptides and validated by comparison with an independent dataset of six membrane-associated peptides and eight integral membrane proteins of known structure and orientation. Comparison of the insertion energy of alpha-helical model peptides with the experimental values from the biological hydrophobicity scale of Hessa et al. gave a correlation of 93% with a mean unsigned error of 0.64 kcal/mol, when charged residues were ignored. The membrane insertion energy was found to be dependent on residue position. This effect is particularly pronounced for charged and polar residues, which strongly prefer interfacial locations. All integral membrane proteins investigated orient and insert correctly into the implicit-membrane model. Remarkably, the membrane model correctly predicts a partially inserted configuration for the monotopic membrane protein cyclooxygenase, matching experimental and theoretical predictions. To test the applicability and usefulness of the implicit-membrane method, molecular simulations of influenza A M2 as well as the glycophorin A dimer were performed. Both systems remain structurally stable and integrated into the membrane
Membrane proteins bind lipids selectively to modulate their structure and function.
No full textPrevious studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane protein structure and/or function. We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding
Amino acid distributions in integral membrane protein structures.
No full textAdvances in structure determination of membrane proteins enable analysis of the propensities of amino acids in extramembrane versus transmembrane locations to be performed on the basis of structure rather than of sequence and predicted topology. Using 29 available structures of integral membrane proteins with resolutions better than 4 A the distributions of amino acids in the transmembrane domains were calculated. The results were compared to analysis based on just the sequences of the same transmembrane alpha-helices and significant differences were found. The distribution of residues between transmembrane alpha-helices and beta-strands was also compared. Large hydrophobic (Phe, Leu, Ile, Val) residues showed a clear preference for the protein surfaces facing the lipids for beta-barrels, but in alpha-helical proteins no such preference was seen, with these residues equally distributed between the interior and the surface of the protein. A notable exception to this was alanine, which showed a slight preference for the interior of alpha-helical membrane proteins. Aromatic residues were found to follow saddle-like distributions preferring to be located in the lipid/water interfaces. The resultant 'aromatic belts' were spaced more closely for beta-barrel than for alpha-helical membrane proteins. Charged residues could be shown to generally avoid surfaces facing the bilayer although they were found to occur frequently in the transmembrane region of beta-barrels. Indeed detailed comparison between alpha-helical and beta-barrel proteins showed many qualitative differences in residue distributions. This suggests that there may be subtle differences in the factors stabilising beta-barrels in bacterial outer membranes and alpha-helix bundles in all other membranes
Receiver Windowing Design for Narrowband Interference Mitigation in MB-OFDM UWB System
No full textIn 2005, the WiMedia Alliance working with the European Computer Manufacturers Association (ECMA) announced the establishment of the WiMedia MB-OFDM (Multiband Orthogonal Frequency Division Multiplexing) UWB radio platform as their global UWB standard. It was also chosen as the physical layer (PHY) of high data rate wireless specifications for high speed Wireless USB (W-USB), Bluetooth 3.0 and Wireless High-Definition Media Interface (HDMI). However, due to the low power and wide bandwidth nature of UWB systems, in-band narrowband interference (NBI) may hinder the receiver performance. This thesis presents an analysis of NBI impact on the MB-OFDM system for UWB communication. The intent of our analysis is to provide practical solutions for interference mitigation under different NBI models. In our work, a new receiver windowing for zero padding (ZP) OFDM system is proposed to reduce NBI spreading in the MB-OFDM UWB system. Simulations demonstrate the effectiveness of windowing under different NBI models.Microelectronics & Computer EngineeringElectrical Engineering, Mathematics and Computer Scienc
Altered immunolocalization of FGF23 in murine femora metastasized with human breast carcinoma MDA-MB-231 cells
No full textIntroduction After the onset of bone metastasis, tumor cells appear to modify surrounding microenvironments for their benefit, and particularly, the levels of circulating fibroblast growth factor (FGF) 23 in patients with tumors have been highlighted. Materials and methods We have attempted to verify if human breast carcinoma MDA-MB-231 cells metastasized in the long bone of nu/nu mice would synthesize FGF23. Serum concentrations of calcium, phosphate (Pi) and FGF23 were measured in control nu/nu mice, bone-metastasized mice, and mice with mammary gland injected with MDA-MB-231 cells mimicking primary mammary tumors. Results and conclusions MDA-MB-231 cells revealed intense FGF23 reactivity in metastasized lesions, whereas MDA-MB-231 cells cultured in vitro or when injected into the mammary glands (without bone metastasis) showed weak FGF23 immunoreactivity. Although the bone-metastasized MDA-MB-231 cells abundantly synthesized FGF23, osteocytes adjacent to the FGF23-immunopositive tumors, unlike intact osteocytes, showed no FGF23. Despite significantly elevated serum FGF23 levels in bone-metastasized mice, there was no significant decrease in the serum Pi concentration when compared with the intact mice and mice with a mass of MDA-MB-231 cells in mammary glands. The metastasized femora showed increased expression and FGFR1 immunoreactivity in fibroblastic stromal cells, whereas femora of control mice showed no obvious FGFR1 immunoreactivity. Taken together, it seems likely that MDA-MB-231 cells synthesize FGF23 when metastasized to a bone, and thus affect FGFR1-positive stromal cells in the metastasized tumor nest in a paracrine manner
ASIC FFT processor for MB-OFDM UWB system
No full textThe physical layer (PHY) standard of Multi-band Orthogonal Frequency Division Multiplexing (MB-OFDM) Ultra Wideband (UWB) system was defined by ECMA International. In this standard, the data sampling rate from the analog-to-digital converter to the physical layer is up to 528 Msample/s. Therefore, it is a challenge to realize the physical layer of the UWB system-especially the components with high computational complexity in Very Large Scale Integration (VLSI) implementation. Fast Fourier Transform (FFT) block is one of these components. FFT plays an important role in Multi-band OFDM UWB system, which is the demodulation block of OFDM signals. The purpose of this project is to design an Application Specific Integrated Circuit (ASIC) FFT solution for this system. The specification is defined from the system analysis and literature research. All the design choices and considerations are concluded and explained.Based on the algorithm and architecture analysis, a novel Radix22Parallel processor is proposed, which is a small-area and low-power-consumption solution for MB-OFDM UWB system. Both Field Programmable Gate Array (FPGA) and ASIC targeted synthesis results of this architecture are presented.Electrical Engineering, Mathematics and Computer Scienc
Characterization of the tertiary structure of the de novo designed protein MB-1
No full textMilk Bundle-1 (MB-1) is a de novo designed protein with 100 amino acids, having a molecular weight of 11.4 kilodaltons. MB-1 is enriched with 57% of selected essential amino acids (methionine, threonine, lysine and leucine), which are known to be limiting in dairy cattle. Recently, on the basis of a digestibility study, MB-1 was predicted to be unstable in rumen conditions.Characterization of the protein's structure was achieved using fluorescence spectroscopy (steady state measurements). MB-1 contains one tyrosine at position 62, expected to be in position "d" of helix III, in the hydrophobic core. Data obtained using fluorescence quenching indicates that the tyrosine is protected from the solvent in the putative hydrophobic core, as per design.Once it was established that MB-1 was not misfolded, further experiments were done to assess the fluidity of its hydrophobic core. For this, the amphiphillic dye ANSA was used. Results obtained for MB-1 compare favourably to those of many natural proteins, suggesting that MB-1 has achieved some degree of nativeness. Interestingly, MB-1 was found to exclude ANSA from its hydrophobic core more efficiently than all other de novo designed proteins reported to date.Finally, an analysis of folding thermodynamics of MB-1 was attempted. It was found that the fluorescence intensity of tyrosine was not sensitive to unfolding, making thermodynamic data impossible to obtain.Analysis of the data on MB-1 as compared to other natural proteins indicates that MB-1 is folded and compact. The lack of resistance to proteases must be caused by other factors other than the lack of compactness or misfolding. (Abstract shortened by UMI.).Source: Masters Abstracts International, Volume: 36-06, page: 1623.Adviser: Marc Beauregard
Stochastic Lie bracket (derivation, derivation) in MB-algebras
No full textBy a stochastic controller, we make stable the pseudo stochastic Lie bracket (derivation, derivation) in complex MB-algebras. Next, we get an approximation by a stochastic Lie bracket (derivation, derivation) and calculate the maximum error of the estimate. © 2020, The Author(s)
Weerkat: An extensible semantic Wiki
No full textWikis are Web applications that blur the boundaries between readers and authors, allowing non-technical people to author hypertexts through a web interface. A Semantic Wiki is a Wiki that attempts the same thing with the Semantic Web, allowing non-technical users to create semantic resources and/or ontologies. In this paper we characterise the different ways in which a Wiki might support the Semantic Web and present Weerkat, a modular and extensible Wiki that has ontological hypertext support. Key to this has been the design and development of a highly flexible Wiki architecture which allows easy modification and augmentation of functionality
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