Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The influence of two-dimensional organization on peptide conformation.

ABSTRACT: Molecular crowding plays a significant role in regulating molecular conformation in cellular environments. It is also likely to be important wherever high molecular densities are required, for example in surface-phase studies, in which molecular densities generally far exceed those observed in solution. Using on-surface circular dichroism (CD) spectroscopy, we have investigated the structure of a synthetic peptide assembled into a highly packed monolayer. The immobilized peptide undergoes a structural transition between ?-helical and random coil conformation upon changes in pH and ionic concentration, but critically the threshold for conformational change is altered dramatically by molecular crowding within the peptide monolayer. This study highlights the often overlooked role molecular crowding plays in regulating molecular structure and function in surface-phase studies of biological molecules.

SUBMITTER: White SJ

PROVIDER: S-EPMC4506555 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The influence of two-dimensional organization on peptide conformation.

White Simon J SJ Johnson Steven D SD Sellick Mark A MA Bronowska Agnieszka A Stockley Peter G PG Wälti Christoph C

Angewandte Chemie (International ed. in English) 20141120 3

Molecular crowding plays a significant role in regulating molecular conformation in cellular environments. It is also likely to be important wherever high molecular densities are required, for example in surface-phase studies, in which molecular densities generally far exceed those observed in solution. Using on-surface circular dichroism (CD) spectroscopy, we have investigated the structure of a synthetic peptide assembled into a highly packed monolayer. The immobilized peptide undergoes a stru ...[more]

PMID: 25413024

Similar Datasets

Two-Dimensional Crowding Uncovers a Hidden Conformation of ?-Synuclein.

Project description:The intrinsically disordered protein (IDP), ?-synuclein (?S), is well-known for phospholipid membrane binding-coupled folding into tunable helical conformers. Here, using single-molecule experiments in conjunction with ensemble assays and a theoretical model, we present a unique case demonstrating that the interaction-folding landscape of ?S can be tuned by two-dimensional (2D) crowding through simultaneous binding of a second protein on the bilayer surface. Unexpectedly, the experimental data show a clear deviation from a simple competitive inhibition model, but are consistent with a bimodal inhibition mechanism wherein membrane binding of a second protein (a membrane interacting chaperone, Hsp27, in this case) differentially inhibits two distinct modules of ?S-membrane interaction. As a consequence, ?S molecules are forced to access a hidden conformational state on the phospholipid bilayer in which only the higher-affinity module remains membrane-bound. Our results demonstrate that macromolecular crowding in two dimensions can play a significant role in shaping the conformational landscape of membrane-binding IDPs with multiple binding modes.

| S-EPMC5166577 | biostudies-literature

Peptide conformation and supramolecular organization in amylin fibrils: constraints from solid-state NMR.

Project description:The 37-residue amylin peptide, also known as islet amyloid polypeptide, forms fibrils that are the main peptide or protein component of amyloid that develops in the pancreas of type 2 diabetes patients. Amylin also readily forms amyloid fibrils in vitro that are highly polymorphic under typical experimental conditions. We describe a protocol for the preparation of synthetic amylin fibrils that exhibit a single predominant morphology, which we call a striated ribbon, in electron microscopy and atomic force microscopy images. Solid-state nuclear magnetic resonance (NMR) measurements on a series of isotopically labeled samples indicate a single molecular structure within the striated ribbons. We use scanning transmission electron microscopy and several types of one- and two-dimensional solid-state NMR techniques to obtain constraints on the peptide conformation and supramolecular structure in these amylin fibrils and to derive molecular structural models that are consistent with the experimental data. The basic structural unit in amylin striated ribbons, which we call the protofilament, contains four layers of parallel beta-sheets, formed by two symmetric layers of amylin molecules. The molecular structure of amylin protofilaments in striated ribbons closely resembles the protofilament in amyloid fibrils with a similar morphology formed by the 40-residue beta-amyloid peptide that is associated with Alzheimer's disease.

| S-EPMC2562526 | biostudies-literature

Cubes to Cubes: Organization of MgO Particles into One-Dimensional and Two-Dimensional Nanostructures.

Project description:Developing simple, inexpensive, and environmentally benign approaches to integrate morphologically well-defined nanoscale building blocks into larger high surface area materials is a key challenge in materials design and processing. In this work, we investigate the fundamental surface phenomena between MgO and water (both adsorption and desorption) with particles prepared via a vapor-phase process (MgO nanocubes) and a modified aerogel process (MgO(111) nanosheets). Through these studies, we unravel a strategy to assemble individual MgO nanoparticles into extended faceted single-crystalline MgO nanosheets and nanorods with well-defined exposed surfaces and edges. This reorganization can be triggered by the presence of H2O vapor or bulk liquid water. Water adsorption and the progressive conversion of vapor-phase grown oxide particles into hydroxides give rise to either one-dimensional or two-dimensional (1D or 2D) structures of high dispersion and surface area. The resulting Mg(OH)2 lamella with a predominant (001) surface termination are well-suited precursor structures for their topotactic conversion into laterally extended and uniform MgO(111) grain surface configurations. To understand the potential of polar (111) surfaces for faceting and surface reconstruction effects associated with water desorption, we investigated the stability of MgO(111) nanosheets during vacuum annealing and electron beam exposure. The significant surface reconstruction of the MgO(111) surfaces observed shows that adsorbate-free (111)-terminated surfaces of unsupported MgO nanostructures reconstruct rather than remain as charged planes of either three-fold coordinated O2- ion or Mg2+ ions. Thus, here we demonstrate the role water can play in surface formation and reconstruction by bridging wet chemical and surface science inspired approaches.

| S-EPMC8343528 | biostudies-literature

Formation of Colloidal Copper Indium Sulfide Nanosheets by Two-Dimensional Self-Organization.

Project description:Colloidal 2D semiconductor nanosheets (NSs) are an interesting new class of materials due to their unique properties. However, synthesis of these NSs is challenging, and synthesis procedures for materials other than the well-known Pb- and Cd-chalcogenides are still underdeveloped. In this paper, we present a new approach to make copper indium sulfide (CIS) NSs and study their structural and optical properties. The CIS NSs form via self-organization and oriented attachment of 2.5 nm chalcopyrite CuInS2 nanocrystals (NCs), yielding triangular- and hexagonal-shaped NSs with a thickness of ∼3 nm and lateral dimensions ranging from 20 to 1000 nm. The self-organization is induced by fast cation extraction, leading to attractive dipolar interactions between the NCs. Primary amines play a crucial role in the formation of the CIS NSs, both by forming in situ the cation extracting agent, and by preventing the attachment of NCs to the top and bottom facets of the NSs. Moreover, DFT calculations reveal that the amines are essential to stabilize the covellite crystal structure of the product CIS NSs. The NSs are indium-deficient and the off-stoichiometry gives rise to a plasmon resonance in the NIR spectral window.

| S-EPMC6156094 | biostudies-literature

Two-Dimensional Infrared (2DIR) Spectroscopy of the Peptide Beta3s Folding.

Project description:Probing underlying free energy landscape, pathways, and mechanism is the key for understanding protein folding in theory and experiment. Recently time-resolved two-dimensional infrared (2DIR) with femtosecond laser pulses, has emerged as a promising tool for investigating the protein folding dynamics on faster timescales than possible by NMR. We have employed molecular dynamics simulations to compute 2DIR spectra of the folding process of a peptide, Beta3s. Simulated non-chiral and chiral 2DIR signals illustrate the variation of the spectra as the peptide conformation evolves along the free energy landscape. Chiral spectra show stronger changes than the non-chiral signals because cross peaks caused by the formation of the ?-sheet are clearly resolved. Chirality-induced 2DIR may be used to detect the folding of ?-sheet proteins with high spectral and temporal resolution.

| S-EPMC3744343 | biostudies-literature

Two-dimensional vibrational optical probes for peptide fast folding investigation.

Project description:A simulation study shows that early protein folding events may be investigated by using a recently developed family of nonlinear infrared techniques that combine the high temporal and spatial resolution of multidimensional spectroscopy with the chirality-specific sensitivity of amide vibrations to structure. We demonstrate how the structural sensitivity of cross-peaks in two-dimensional correlation plots of chiral signals of an alpha helix and a beta hairpin may be used to clearly resolve structural and dynamical details undetectable by one-dimensional techniques (e.g. circular dichroism) and identify structures indistinguishable by NMR.

| S-EPMC1748155 | biostudies-literature

Two Dimensional Oblique Molecular Packing within a Model Peptide Ribbon Aggregate.

Project description:A10 K (A=alanine, K=lysine) model peptides self-assemble into ribbon-like ?-sheet aggregates. Here, we report an X-ray diffraction investigation on a flow-aligned dispersion of these self-assembly structures. The two-dimensional wide-angle X-ray scattering pattern suggests that peptide pack in a two-dimensional oblique lattice, essentially identical to the crystalline packing of polyalanine, An (for n>4). One side of the oblique unit cell, corresponding to the anti-parallel ?-sheet, is oriented along the ribbon's axis. Together with recently published small angle X-ray scattering data of the same system, this work thus yields a detailed description of the self-assembled ribbon aggregates, down to the molecular length scale. Notably, our results highlight the importance of the crystalline peptide packing within its self-assembly aggregates, which is often neglected.

| S-EPMC7496194 | biostudies-literature

Software lock mass by two-dimensional minimization of peptide mass errors.

Project description:Mass accuracy is a key parameter in proteomic experiments, improving specificity, and success rates of peptide identification. Advances in instrumentation now make it possible to routinely obtain high resolution data in proteomic experiments. To compensate for drifts in instrument calibration, a compound of known mass is often employed. This 'lock mass' provides an internal mass standard in every spectrum. Here we take advantage of the complexity of typical peptide mixtures in proteomics to eliminate the requirement for a physical lock mass. We find that mass scale drift is primarily a function of the m/z and the elution time dimensions. Using a subset of high confidence peptide identifications from a first pass database search, which effectively substitute for the lock mass, we set up a global mathematical minimization problem. We perform a simultaneous fit in two dimensions using a function whose parameterization is automatically adjusted to the complexity of the analyzed peptide mixture. Mass deviation of the high confidence peptides from their calculated values is then minimized globally as a function of both m/z value and elution time. The resulting recalibration function performs equal or better than adding a lock mass from laboratory air to LTQ-Orbitrap spectra. This 'software lock mass' drastically improves mass accuracy compared with mass measurement without lock mass (up to 10-fold), with none of the experimental cost of a physical lock mass, and it integrated into the freely available MaxQuant analysis pipeline ( www.maxquant.org ).

| S-EPMC3231580 | biostudies-literature

Metamorphic protein IscU changes conformation by cis-trans isomerizations of two peptidyl-prolyl peptide bonds.

Project description:IscU from Escherichia coli, the scaffold protein for iron-sulfur cluster biosynthesis and transfer, populates two conformational states with similar free energies and with lifetimes on the order of 1 s that interconvert in an apparent two-state reaction. One state (S) is structured, and the other (D) is largely disordered; however, both play essential functional roles. We report here nuclear magnetic resonance studies demonstrating that all four prolyl residues of apo-IscU (P14, P35, P100, and P101) are trans in the S state but that two absolutely conserved residues (P14 and P101) become cis in the D state. The peptidyl-prolyl peptide bond configurations were determined by analyzing assigned chemical shifts and were confirmed by measurements of nuclear Overhauser effects. We conclude that the S ? D interconversion involves concerted trans-cis isomerization of the N13-P14 and P100-P101 peptide bonds. Although the D state is largely disordered, we show that it contains an ordered domain that accounts for the stabilization of two high-energy cis peptide bonds. Thus, IscU may be classified as a metamorphic protein.

| S-EPMC3567208 | biostudies-literature

Self-Assembly of an ?-Helical Peptide into a Crystalline Two-Dimensional Nanoporous Framework.

Project description:Sequence-specific peptides have been demonstrated to self-assemble into structurally defined nanoscale objects including nanofibers, nanotubes, and nanosheets. The latter structures display significant promise for the construction of hybrid materials for functional devices due to their extended planar geometry. Realization of this objective necessitates the ability to control the structural features of the resultant assemblies through the peptide sequence. The design of a amphiphilic peptide, 3FD-IL, is described that comprises two repeats of a canonical 18 amino acid sequence associated with straight ?-helical structures. Peptide 3FD-IL displays 3-fold screw symmetry in a helical conformation and self-assembles into nanosheets based on hexagonal packing of helices. Biophysical evidence from TEM, cryo-TEM, SAXS, AFM, and STEM measurements on the 3FD-IL nanosheets support a structural model based on a honeycomb lattice, in which the length of the peptide determines the thickness of the nanosheet and the packing of helices defines the presence of nanoscale channels that permeate the sheet. The honeycomb structure can be rationalized on the basis of geometrical packing frustration in which the channels occupy defect sites that define a periodic superlattice. The resultant 2D materials may have potential as materials for nanoscale transport and controlled release applications.

| S-EPMC5739522 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data