ArticleThe journal of physical chemistry. B2010
Ultraviolet spectroscopy of protein backbone transitions in aqueous solution: combined QM and MM simulations.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 63 citations in OpenAlex.
- Effects of TiOBiochemistry and biophysics reports · 2026Article
- Synthesis and optimization of fluoxetine-loaded polymeric nanoparticles for dual therapeutic applications in cancer and depression.Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences · 2025Article
- Thiol, His-His Motif, and the Battle over Cu(II) in the Relationship of CopM Metallophore and OprC Outer Membrane Protein.Inorganic chemistry · 2025Article
- Micellization of Lipopeptides Containing Toll-like Receptor Agonist and Integrin Binding Sequences.ACS applied materials & interfaces · 2024Review
- Determination of Conformational and Functional Stability of Potential Plague Vaccine Candidate in Formulation.Vaccines · 2022Article
- Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides.Molecules (Basel, Switzerland) · 2021Article
- Controlled Supramolecular Assembly Inside Living Cells by Sequential Multistaged Chemical Reactions.Journal of the American Chemical Society · 2020Article
- Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules.Chemical reviews · 2020Review
- Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet.Chemical science · 2017Article
- Exciton circular dichroism couplet arising from nitrile-derivatized aromatic residues as a structural probe of proteins.Analytical biochemistry · 2016Article
- Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory.International journal of molecular sciences · 2015Article
- Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy.The journal of physical chemistry letters · 2014Article
- Disentangling Peptide Configurations via Two-Dimensional Electronic Spectroscopy: Ab Initio Simulations Beyond the Frenkel Exciton Hamiltonian.The journal of physical chemistry letters · 2014Article
- Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding.Physical chemistry chemical physics : PCCP · 2013Article
- Exploring the aggregation propensity of γS-crystallin protein variants using two-dimensional spectroscopic tools.The journal of physical chemistry. B · 2013Article
- Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy.The journal of physical chemistry. A · 2013Article
- Deep UV resonance Raman spectroscopy of β-sheet amyloid fibrils: a QM/MM simulation.The journal of physical chemistry. B · 2011Article
- Distinguishing amyloid fibril structures in Alzheimer's disease (AD) by two-dimensional ultraviolet (2DUV) spectroscopy.Biochemistry · 2011Article
- Probing amyloid fibril growth by two-dimensional near-ultraviolet spectroscopy.The journal of physical chemistry. B · 2011Article
- Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study.Physical chemistry chemical physics : PCCP · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
A generalized approach combining quantum mechanics (QM) and molecular mechanics (MM) calculations is developed to simulate the n --> pi* and pi --> pi* backbone transitions of proteins in aqueous solution. These transitions, which occur in the ultraviolet (UV) at 180-220 nm, provide a sensitive probe for secondary structures. The excitation Hamiltonian is constructed using high-level electronic structure calculations of N-methylacetamide (NMA). Its electrostatic fluctuations are modeled using a new algorithm, EHEF, which combines a molecular dynamics (MD) trajectory obtained with a MM forcefield and electronic structures of sampled MD snapshots calculated by QM. The lineshapes and excitation splittings induced by the electrostatic environment in the experimental UV linear absorption (LA) and circular dichroism (CD) spectra of several proteins in aqueous solution are reproduced by our calculations. The distinct CD features of alpha-helix and beta-sheet protein structures are observed in the simulations and can be assigned to different backbone geometries. The fine structure of the UV spectra is accurately characterized and enables us to identify signatures of secondary structures.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.