Circular and linear dichroism spectroscopy of proteins

Circular dichroism (CD) is an important technique in the structural characterization of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the matrix method, with an accuracy that is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. The vacuum-UV region (below 190 nm), where charge-transfer transitions have an influence on the CD spectra, can be accessed using synchrotron radiation circular dichroism (SRCD) spectroscopy. Calculations of the vacuum-UV CD spectra have been performed for 71 proteins, for which experimental SRCD spectra and X-ray crystal structures are available. The theoretical spectra are calculated considering charge-transfer and side chain transitions, which significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and experimental intensity at 175 nm from 0.12 to 0.79. The influence of the different conformations used for the calculation of charge-transfer transitions is discussed in detail, focussing on the effect in the vacuum-UV. Linear dichroism (LD) provides information on the orientation of molecules but is more challenging to analyze than CD. To aid the interpretation of LD spectra, the calculation of protein LD using the matrix method is established and the results compared to experimental data. The orientations of five prototypical proteins are correctly reproduced by the calculations. Using a simplified approach, matrix method parameter sets for the nucleic bases and naphthalenediimide (NDI) have been created and are used to determine DNA/RNA conformations and to study NDI nanotubes. Finally, to make CD and LD calculations available for the scientific community in an easy-to-use fashion, the web interface DichroCalc is introduced

Circular and linear dichroism spectroscopy of proteins

Circular dichroism (CD) is an important technique in the structural characterization of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the matrix method, with an accuracy that is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. The vacuum-UV region (below 190 nm), where charge-transfer transitions have an influence on the CD spectra, can be accessed using synchrotron radiation circular dichroism (SRCD) spectroscopy. Calculations of the vacuum-UV CD spectra have been performed for 71 proteins, for which experimental SRCD spectra and X-ray crystal structures are available. The theoretical spectra are calculated considering charge-transfer and side chain transitions, which significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and experimental intensity at 175 nm from 0.12 to 0.79. The influence of the different conformations used for the calculation of charge-transfer transitions is discussed in detail, focussing on the effect in the vacuum-UV. Linear dichroism (LD) provides information on the orientation of molecules but is more challenging to analyze than CD. To aid the interpretation of LD spectra, the calculation of protein LD using the matrix method is established and the results compared to experimental data. The orientations of five prototypical proteins are correctly reproduced by the calculations. Using a simplified approach, matrix method parameter sets for the nucleic bases and naphthalenediimide (NDI) have been created and are used to determine DNA/RNA conformations and to study NDI nanotubes. Finally, to make CD and LD calculations available for the scientific community in an easy-to-use fashion, the web interface DichroCalc is introduced

Conformational effects on the Circular Dichroism of Human Carbonic Anhydrase II: a multilevel computational study

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions

Controlling the assembly of coiled-coil peptide nanotubes

An ability to control the assembly of peptide nanotubes (PNTs) would provide biomaterials for applications in nanotechnology and synthetic biology. Recently, we presented a modular design for PNTs using α-helical barrels with tunable internal cavities as building blocks. These first-generation designs thicken beyond single PNTs. Herein we describe strategies for controlling this lateral association, and also for the longitudinal assembly. We show that PNT thickening is pH sensitive, and can be reversed under acidic conditions. Based on this, repulsive charge interactions are engineered into the building blocks leading to the assembly of single PNTs at neutral pH. The building blocks are modified further to produce covalently linked PNTs via native chemical ligation, rendering ca. 100 nm-long nanotubes. Finally, we show that small molecules can be sequestered within the interior lumens of single PNTs

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet

Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation and insights into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures

Anti-antimicrobial Peptides FOLDING-MEDIATED HOST DEFENSE ANTAGONISTS:FOLDING-MEDIATED HOST DEFENSE ANTAGONISTS

Antimicrobial or host defense peptides are innate immune regulators found in all multicellular organisms. Many of them fold into membrane-bound α-helices and function by causing cell wall disruption in microorganisms. Herein we probe the possibility and functional implications of antimicrobial antagonism mediated by complementary coiled-coil interactions between antimicrobial peptides and de novo designed antagonists: anti-antimicrobial peptides. Using sequences from native helical families such as cathelicidins, cecropins, and magainins we demonstrate that designed antagonists can co-fold with antimicrobial peptides into functionally inert helical oligomers. The properties and function of the resulting assemblies were studied in solution, membrane environments, and in bacterial culture by a combination of chiroptical and solid-state NMR spectroscopies, microscopy, bioassays, and molecular dynamics simulations. The findings offer a molecular rationale for anti-antimicrobial responses with potential implications for antimicrobial resistance

Self-assembly of a model amphiphilic oligopeptide incorporating an arginine headgroup

The self-assembly in aqueous solution of the alanine-rich peptide A12R2 containing twelve alanine residues and two arginine residues has been investigated. This oligomeric peptide was synthesized via NCA-polymerization methods. The surfactant-like peptide is found via FTIR to form antiparallel dimers which aggregate into twisted fibrils, as revealed by cryogenic-transmission electron microscopy. The fibril substructure is probed via detailed X-ray scattering experiments, and are uniquely comprised of twisted tapes only 5 nm wide, set by the width of the antiparallel A12R2 dimers. The packing of the alanine residues leads to distinct “b-sheet” spacings compared to those for amyloid-forming peptides. For this peptide, b-sheet structure coexists with some a-helical content. These ultrafine amyloid fibrils present arginine at high density on their surfaces, and this may lead to applications in nanobiotechnology

Exploiting Anisotropy of Plasmonic Nanostructures with Polarization-Modulation Infrared Linear Dichroism Microscopy (μPM-IRLD).

Metallic nanostructures that exhibit plasmon resonances in the mid-infrared range are of particular interest for a variety of optical processes where the infrared excitation and/or emission could be enhanced. This plasmon-mediated enhancement can potentially be used towards highly sensitive detection of an analyte(s) by techniques such as surface-enhanced infrared absorption (SEIRA). To maximize the SEIRA enhancement, it is necessary to prepare highly tuned plasmonic resonances over a defined spectral range that can span over several microns. Noteworthy, nanostructures with anisotropic shapes exhibit multiple resonances that can be exploited by controlling the polarization of the input light. This study demonstrates the role of polarization-modulation infrared linear dichroism coupled to microscopy measurements (μPM-IRLD) as a powerful means to explore the optical properties of anisotropic nanostructures. Quantitative μPM-IRLD measurements were conducted on a 2 series of dendritic fractals as model structures to explore the role of structural anisotropy on the resulting surface-enhanced infrared absorption and sensing application. Once functionalized with an analyte, the μPM-IRLD SEIRA results highlight that it is possible to selectively enhance further vibrational modes of analytes making use of the structural anisotropy of the metallic nanostructure

A Close Eye on the Eagle-Eyed Visual Acuity Hypothesis of Autism

Autism spectrum disorders (ASD) have been associated with sensory hypersensitivity. A recent study reported visual acuity (VA) in ASD in the region reported for birds of prey. The validity of the results was subsequently doubted. This study examined VA in 34 individuals with ASD, 16 with schizophrenia (SCH), and 26 typically developing (TYP). Participants with ASD did not show higher VA than those with SCH and TYP. There were no substantial correlations of VA with clinical severity in ASD or SCH. This study could not confirm the eagle-eyed acuity hypothesis of ASD, or find evidence for a connection of VA and clinical phenotypes. Research needs to further address the origins and circumstances associated with altered sensory or perceptual processing in ASD