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Nature Protocols 2006Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using...
Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that measurements may be made on multiple samples containing < or =20 microg of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.
Topics: Algorithms; Artificial Intelligence; Buffers; Circular Dichroism; Linear Models; Peptides; Protein Structure, Secondary; Proteins; Statistics as Topic
PubMed: 17406547
DOI: 10.1038/nprot.2006.202 -
ACS Nano Oct 2021Chiral nanophotonic materials are promising candidates for biosensing applications because they focus light into nanometer dimensions, increasing their sensitivity to... (Review)
Review
Chiral nanophotonic materials are promising candidates for biosensing applications because they focus light into nanometer dimensions, increasing their sensitivity to the molecular signatures of their surroundings. Recent advances in nanomaterial-enhanced chirality sensing provide detection limits as low as attomolar concentrations (10 M) for biomolecules and are relevant to the pharmaceutical industry, forensic drug testing, and medical applications that require high sensitivity. Here, we review the development of chiral nanomaterials and their application for detecting biomolecules, supramolecular structures, and other environmental stimuli. We discuss superchiral near-field generation in both dielectric and plasmonic metamaterials that are composed of chiral or achiral nanostructure arrays. These materials are also applicable for enhancing chiroptical signals from biomolecules. We review the plasmon-coupled circular dichroism mechanism observed for plasmonic nanoparticles and discuss how hotspot-enhanced plasmon-coupled circular dichroism applies to biosensing. We then review single-particle spectroscopic methods for achieving the ultimate goal of single-molecule chirality sensing. Finally, we discuss future outlooks of nanophotonic chiral systems.
Topics: Circular Dichroism; Nanoparticles; Nanostructures; Nanotechnology
PubMed: 34609836
DOI: 10.1021/acsnano.1c04992 -
International Journal of Molecular... Oct 2021A useful tool to analyze the ligands and/or environmental contribution to protein stability is represented by the Synchrotron Radiation Circular Dichroism...
A useful tool to analyze the ligands and/or environmental contribution to protein stability is represented by the Synchrotron Radiation Circular Dichroism UV-denaturation assay that consists in the acquisition of several consecutive repeated far-UV SRCD spectra. Recently we demonstrated that the prevailing mechanism of this denaturation involves the generation of free radicals and reactive oxygen species (ROS). In this work, we analyzed the effect of buffering agents commonly used in spectroscopic measurements, including MOPS (3-(N-morpholino) propanesulfonic acid), HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), TRIS-HCl (tris-hydroxymethil aminomethane hydrochloride), and phosphate, on the efficiency of protein denaturation caused by exposure to UV radiation. Fluorescence experiments confirmed the presence of ROS and were used to determine the rate of ROS generation. Our results indicate that the efficiency of the denaturation process is strongly influenced by the buffer composition with MOPS and HEPES acting also as scavengers and that the presence of proteins itself influenced the ROS formation rate.
Topics: Biological Assay; Buffers; Circular Dichroism; Free Radicals; Ligands; Protein Denaturation; Protein Stability; Proteins; Reactive Oxygen Species; Synchrotrons; Ultraviolet Rays
PubMed: 34768758
DOI: 10.3390/ijms222111325 -
Optics Express Aug 2022Chiral metamaterials with circular dichroism (CD) or asymmetric transmission (AT) draw enormous attention for their attractive applications in polarization transformers,...
Chiral metamaterials with circular dichroism (CD) or asymmetric transmission (AT) draw enormous attention for their attractive applications in polarization transformers, circular polarizers, and biosensing. In this study, a feasible trilayer chiral metamaterials (TCM) is designed and investigated in theory and simulation. The proposed TCM is composed of a nanoslit layer and a Babinet-complementary nanorod layer separated by a nanoslit spacer. Owing to symmetry breaking by the tilted nanoslit in metal film, the TCM shows simultaneous CD and AT effects in the near-infrared region. The simulated electric charge distributions prove that the chirality arises from the excitation of asymmetric electric dipole resonant modes due to the coupling of adjacent unit cells. Moreover, CD and AT can be tuned by the tilted angle of the nanoslit and the thickness of the spacer, the fitting functions of which are consistent with the theoretical formulas based on transmittance matrix analysis. The proposed nanostructure offers a potential strategy for manipulating metamaterials with simultaneous CD and AT effects, allowing a multitude of exciting applications such as ultra-sensitive polarization transformer and biosensor.
Topics: Biosensing Techniques; Circular Dichroism; Metals; Nanostructures
PubMed: 36242144
DOI: 10.1364/OE.464798 -
Chemical Society Reviews Aug 2021Circular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24 000 papers published in the... (Review)
Review
Circular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24 000 papers published in the past decade have included CD characterisations of proteins; many of those studies have also included other complementary chemical, biophysical, and computational chemistry methods. This tutorial review describes the background to the technique of CD spectroscopy and good practice methods for high quality data collection. It specifically focuses on both established and new methods and tools available for experimental design and interpretation, data processing, visualisation, analysis, validation, archiving, and accession, including tools developed to enhance the complementarity of this method with other structural and chemical biology studies.
Topics: Biochemistry; Circular Dichroism; Humans; Proteins
PubMed: 34132259
DOI: 10.1039/d0cs00558d -
Nucleic Acids Research Jan 2023The Nucleic Acid Circular Dichroism Database (NACDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD...
The Nucleic Acid Circular Dichroism Database (NACDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data about nucleic acids, and the associated experimental metadata, structural models, and links to literature. NACDDB covers CD data for various nucleic acid molecules, including DNA, RNA, DNA/RNA hybrids, and various nucleic acid derivatives. The entries are linked to primary sequence and experimental structural data, as well as to the literature. Additionally, for all entries, 3D structure models are provided. All entries undergo expert validation and curation procedures to ensure completeness, consistency, and quality of the data included. The NACDDB is open for submission of the CD data for nucleic acids. NACDDB is available at: https://genesilico.pl/nacddb/.
Topics: Circular Dichroism; Databases, Nucleic Acid; Synchrotrons; Nucleic Acids
PubMed: 36280237
DOI: 10.1093/nar/gkac829 -
Molecules (Basel, Switzerland) Sep 2018Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule... (Review)
Review
Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed.
Topics: Circular Dichroism; Molecular Conformation; Signal Processing, Computer-Assisted; Stereoisomerism
PubMed: 30235902
DOI: 10.3390/molecules23092404 -
Molecules (Basel, Switzerland) Jan 2021A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation...
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.
Topics: Circular Dichroism; Peptides; Protein Conformation; Spectrophotometry, Ultraviolet
PubMed: 33451152
DOI: 10.3390/molecules26020396 -
Photosynthesis Research 2009The efficiency of photosynthetic light energy conversion depends largely on the molecular architecture of the photosynthetic membranes. Linear- and circular-dichroism... (Review)
Review
The efficiency of photosynthetic light energy conversion depends largely on the molecular architecture of the photosynthetic membranes. Linear- and circular-dichroism (LD and CD) studies have contributed significantly to our knowledge of the molecular organization of pigment systems at different levels of complexity, in pigment-protein complexes, supercomplexes, and their macroassemblies, as well as in entire membranes and membrane systems. Many examples show that LD and CD data are in good agreement with structural data; hence, these spectroscopic tools serve as the basis for linking the structure of photosynthetic pigment-protein complexes to steady-state and time-resolved spectroscopy. They are also indispensable for identifying conformations and interactions in native environments, and for monitoring reorganizations during photosynthetic functions, and are important in characterizing reconstituted and artificially constructed systems. This educational review explains, in simple terms, the basic physical principles, and theory and practice of LD and CD spectroscopies and of some related quantities in the areas of differential polarization spectroscopy and microscopy.
Topics: Biopolymers; Cell Membrane; Circular Dichroism; Light; Photosynthesis; Pigments, Biological
PubMed: 19418239
DOI: 10.1007/s11120-009-9424-4 -
Molecules (Basel, Switzerland) Feb 2021Despite significant interest, the chiroptical properties of subporphyrins have rarely been investigated because chiral subporphyrins are elusive. Here, inherently chiral...
Despite significant interest, the chiroptical properties of subporphyrins have rarely been investigated because chiral subporphyrins are elusive. Here, inherently chiral subporphyrins are elaborated by forming a fused pyran ring at the periphery of an AB-type -aryl-substituted subporphyrin. Their circular dichroism (CD) properties are largely affected by the peripheral substituents and the dihedral angles between the -aryl substituents and the subporphyrin core: the β-perbromo subporphyrin with an orthogonal arrangement of the -phenyl substituents to the subporphyrin core exhibits weak CD signals corresponding to the Q bands, whereas the unsubstituted species with smaller dihedral angles shows relatively intense CD signals. A detailed structure-property relationship of these chiral subporphyrins was elucidated by time-dependent (TD) DFT calculations. This study reveals that the CD properties of chiral subporphyrins can be controlled by peripheral substitution and -aryl substituents.
Topics: Boron Compounds; Circular Dichroism; Density Functional Theory; Molecular Conformation; Porphyrins; Stereoisomerism
PubMed: 33672731
DOI: 10.3390/molecules26041140