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A peptide's perspective of water dynamics

Ayanjeet Ghosh, Robin M. Hochstrasser
2011 Chemical Physics  
local water at a residue level in proteins.  ...  The 2D IR spectroscopy has already enabled structural aspects of the peptide backbone to be determined through its ability to measure the coupling between different amide-I modes.  ...  Daniel Kuroda for helpful discussions and carrying out the DFT calculations on the water-amide configurations.  ... 
doi:10.1016/j.chemphys.2011.07.018 pmid:22844177 pmcid:PMC3404498 fatcat:5aqvhobvmzex3fumjtohqi7yku

WW Domain Folding Complexity Revealed by Infrared Spectroscopy

Caitlin M. Davis, R. Brian Dyer
2014 Biochemistry  
Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone.  ...  This study demonstrates that using multiple complementary probes enhances the interpretation of protein folding dynamics.  ...  A bandwidth of 2 nm and a scan rate of 50 nm/ min were used for spectral acquisition.  ... 
doi:10.1021/bi500556h pmid:25121968 pmcid:PMC4151701 fatcat:mgg54hllwzhxtbrbqohq5c3txy

Probing Biological Water Using Terahertz Absorption Spectroscopy [chapter]

Rajib Kumar Mitra, Dipak Kumar Palit
2021 Terahertz Technology [Working Title]  
THz spectroscopy has also been successfully applied to study the effect of modulation of the physical conditions, like temperature, pH, concentration of proteins and chemical additives, on the structure  ...  While NMR, X-ray and UV–vis-IR spectroscopic techniques have been found inadequate for describing the dynamics of the thick (20–40 Å) sheath of hydration layer around biomolecules, recently developed THz  ...  The change in protein hydration is also found to trace its secondary structure rupture and the exposure of hydrophobic moieties accordingly changes the protein hydration.  ... 
doi:10.5772/intechopen.97603 fatcat:zhkvh6motfg2hkwacy3jazn6zi

Photoisomerization in rhodopsin

H Kandori, Y Shichida, T Yoshizawa
2001 Biochemistry (Moscow)  
Femtosecond fluorescence spectroscopy directly captured excited-state dynamics of rhodopsin, so that both coherent reaction process and unreacted excited state were observed.  ...  This article reviews the primary reaction processes in rhodopsin, a photoreceptive pigment for twilight vision.  ...  Figure 6 shows the secondary structural model of bovine rhodopsin.  ... 
pmid:11743865 fatcat:7ifjfc6gtrex7hulplu6v4vaqm

Structural Disorder of Folded Proteins: Isotope-Edited 2D IR Spectroscopy and Markov State Modeling

Carlos R. Baiz, Andrei Tokmakoff
2015 Biophysical Journal  
Structural interpretation of the amide I line shapes is enabled by spectral simulations carried out on structures extracted from a recent Markov state model.  ...  The conformational heterogeneity of the N-terminal domain of the ribosomal protein L9 (NTL9 1-39 ) in its folded state is investigated using isotope-edited two-dimensional infrared spectroscopy.  ...  model and for insightful discussions.  ... 
doi:10.1016/j.bpj.2014.12.061 pmid:25863066 pmcid:PMC4390782 fatcat:x3mixndwkjfyjplx2vmcpkntjy

The C-Terminal Sequence of Several Human Serine Proteases Encodes Host Defense Functions

Gopinath Kasetty, Praveen Papareddy, Martina Kalle, Victoria Rydengård, Björn Walse, Bo Svensson, Matthias Mörgelin, Martin Malmsten, Artur Schmidtchen
2011 Journal of Innate Immunity  
These sequences were aligned using ClustalW using Blosum 69 protein weight matrix settings.  ...  The most important descriptor of the model was the peptide net charge, while other less important descriptors were related to the hydrophobicity as well as electrostatic and hydrophobic moments.  ... 
doi:10.1159/000327016 pmid:21576923 fatcat:n2rhzh4qjrgazjydfewxfhsdzu

Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces

Jacob Monroe, Mikayla Barry, Audra DeStefano, Pinar Aydogan Gokturk, Sally Jiao, Dennis Robinson-Brown, Thomas Webber, Ethan J. Crumlin, Songi Han, M. Scott Shell
2020 Annual Review of Chemical and Biomolecular Engineering  
One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity  ...  Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.  ...  MD simulations have also been used to identify dielectric spectral components corresponding to single-molecule motion (slower) and collective motion (faster) in protein powders (78) .  ... 
doi:10.1146/annurev-chembioeng-120919-114657 pmid:32169001 fatcat:gkqsruzy7be5hfm6b5yfsndywm

The IsdC Protein fromStaphylococcus aureusUses a Flexible Binding Pocket to Capture Heme

Valerie A. Villareal, Rosemarie M. Pilpa, Scott A. Robson, Evgeny A. Fadeev, Robert T. Clubb
2008 Journal of Biological Chemistry  
IsdC partially buries protoporphyrin within a large hydrophobic pocket that is located at the end of its ␤-barrel structure.  ...  Staphylococcus aureus scavenges heme-iron from host hemoproteins using iron-regulated surface determinant (Isd) proteins.  ...  Acknowledgments-We thank Tim Anderson for assistance with the relaxation data analysis. We also thank Dr. Robert Peterson for assistance with NMR experiments.  ... 
doi:10.1074/jbc.m801126200 pmid:18715872 pmcid:PMC2581589 fatcat:oae3z3xuwnbmrmlgfgbgmv3bti

Two-Dimensional Infrared Spectroscopy as a Probe of the Solvent Electrostatic Field for a Twelve Residue Peptide†

Jianping Wang, Wei Zhuang, Shaul Mukamel, Robin Hochstrasser
2008 Journal of Physical Chemistry B  
Spectral simulations using both maps predict the main spectral features of the linear IR and 2D IR experimental results of the 13 C-labeled and -unlabeled hairpin.  ...  Both maps predict a set of nondegenerate local amide-I mode transition energies for the hairpin.  ...  Even very simplified empirical theories of peptide IR spectra 10, 11 often capture approximately the spectral shapes for particular secondary structures if the coupling constants happen to be very large  ... 
doi:10.1021/jp075683k pmid:18078331 pmcid:PMC2888599 fatcat:awkls47cobavxpdmalxre3wzqy

Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy

Ayanjeet Ghosh, Joshua S. Ostrander, Martin T. Zanni
2017 Chemical Reviews  
Proteins exhibit structural fluctuations over decades of time scales.  ...  Polarization Controlled 2D IR To Determine Structure Since 2D IR is a coherent spectroscopy, all of the interacting fields have polarizations that can be independently controlled.  ...  IR spectroscopy has been exceptionally successful in studying the secondary structure of proteins.  ... 
doi:10.1021/acs.chemrev.6b00582 pmid:28060489 pmcid:PMC5500453 fatcat:o32nmxs47zfltokyazoiwbbnmm

Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin

V. V. Krishnan, Edmond Y. Lau, Justin Yamada, Daniel P. Denning, Samir S. Patel, Michael E. Colvin, Michael F. Rexach, Philip E. Bourne
2008 PLoS Computational Biology  
by anyone for any lawful purpose.  ...  Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116.  ...  Secondary structure analysis: For the final 3 ns of each simulation, the structure was analyzed every 1 ps using a standard program for identifying secondary structure from atomic coordinates (Define Secondary  ... 
doi:10.1371/journal.pcbi.1000145 pmid:18688269 pmcid:PMC2475668 fatcat:vnm4o2zscbd2fkkjmyxs5o66xi

Vibrations, quanta and biology

S.F. Huelga, M.B. Plenio
2013 Contemporary physics (Print)  
photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for  ...  networks are subjected to are determined and tuned mainly via the secondary protein structure.  ...  Hence, in various circumstances it may be essential to reduce the level of noise for example by protecting a molecule inside a protein structure or a hydrophobic binding pocket.  ... 
doi:10.1080/00405000.2013.829687 fatcat:wpiuvl4tfref3bhxwinbs4gbyu

Spectral Signatures of Heterogeneous Protein Ensembles Revealed by MD Simulations of 2DIR Spectra

Ziad Ganim, Andrei Tokmakoff
2006 Biophysical Journal  
A model for the calculation of amide I FTIR and 2DIR spectra taking into account fluctuations in hydrogen bonding and structure from molecular dynamics (MD) simulations is tested on three systems.  ...  With the ability to accurately predict 2DIR spectra from atomistic simulations, new opportunities to test force fields and mechanistic predictions from MD are revealed.  ...  and a fast dynamic probe of protein secondary structure.  ... 
doi:10.1529/biophysj.106.088070 pmid:16844758 pmcid:PMC1562382 fatcat:srwccdcxbvhy5kojo2kwkpxyni

Static Disorder in Excitation Energies of the Fenna–Matthews–Olson Protein: Structure-Based Theory Meets Experiment

Marten L. Chaillet, Florian Lengauer, Julian Adolphs, Frank Müh, Alexander S. Fokas, Daniel J. Cole, Alex W. Chin, Thomas Renger
2020 Journal of Physical Chemistry Letters  
Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein  ...  The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site  ...  of mostly β-sheet secondary structures ( Figure 1 ).  ... 
doi:10.1021/acs.jpclett.0c03123 pmid:33227205 pmcid:PMC7751012 fatcat:exak5v44kbfbnpcpyei3yilyfi

High-yield Production of Amyloid-β Peptide Enabled by a Customized Spider Silk Domain

Axel Abelein, Gefei Chen, Kristīne Kitoka, Rihards Aleksis, Filips Oleskovs, Médoune Sarr, Michael Landreh, Jens Pahnke, Kerstin Nordling, Nina Kronqvist, Kristaps Jaudzems, Anna Rising (+2 others)
2020 Scientific Reports  
We observe that NTs from different spidroins have co-evolved with their respective repeat region, and now use an NT that is distantly related to previously used NTs, for efficient recombinant production  ...  During storage in the silk gland, the N-terminal domain (NT) of spider silk proteins (spidroins) keeps the aggregation-prone repetitive region in solution at extreme concentrations.  ...  For protein structure determination, first the spectral peaks are assigned.  ... 
doi:10.1038/s41598-019-57143-x pmid:31937841 pmcid:PMC6959368 fatcat:ir6dgi65k5e7hm5pszla2xb2iu
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