Benjamin M. Bulheller

DichroCalc—circular and linear dichroism online

MOTIVATION Circular dichroism (CD) is widely used in studies of protein folding. The CD spectrum of a protein can be estimated from its structure alone, using the well-established matrix method. In the last decade, a related spectroscopy, linear dichroism (LD), has been increasingly applied to study the orientation of proteins in solution. However, matrix method calculations of LD spectra have not been presented before. DichroCalc makes both CD and LD calculations available in an easy-to-use fashion. RESULTS DichroCalc can be used without registration and calculates CD and LD spectra using a variety of matrix method parameters. PDB files can be uploaded as input or retrieved via their PDB code and a Perl-based parser is offered for easy handling of PDB files. AVAILABILITY http://comp.chem.nottingham.ac.uk/dichrocalc and http://comp.chem.nottingham.ac.uk/parsepdb.

Ultraviolet spectroscopy of protein backbone transitions in aqueous solution: combined QM and MM simulations.

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.

Electronic structure and circular dichroism spectroscopy of naphthalenediimide nanotubes.

Amino acid derivatives of naphthalenediimide (NDI) form non-covalent polymers, which assemble into helical nanotubes through hydrogen bonding. The two enantiomers possess distinct circular dichroism (CD) spectra, but the bands could not be entirely ascribed to the effects of the monomer or a supramolecular structure. We calculate the CD of oligomers, using the (exciton) matrix method, based on ab initio results for the monomer. Several features in the experimental spectrum could be reproduced well and allow assignment of the electronic states of the oligomeric structure. The calculations provide evidence that the oligomer structures in the solid state and the solution phase are equivalent. The calculated spectra show a dependence on the oligomer length, which potentially could be exploited for the experimental characterization of the length of the helical nanotubes.

Flow Linear Dichroism of Some Prototypical Proteins

Flow linear dichroism (LD) spectroscopy provides information on the orientation of molecules in solution and hence on the relative orientation of parts of molecules. Long molecules such as fibrous proteins can be aligned in Couette flow cells and characterized using LD. We have measured using Couette flow and calculated from first principles the LD of proteins representing prototypical secondary structure classes: a self-assembling fiber and tropomyosin (all-alpha-helical), FtsZ (an alphabeta protein), an amyloid fibril (beta-sheet), and collagen [poly(proline)II helices]. The combination of calculation and experiment allows elucidation of the protein orientation in the Couette flow and the orientation of chromophores within the protein fibers.

Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra.

Circular dichroism (CD) is widely used in the structural characterization and secondary structure determination of proteins. 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. Recently, charge-transfer transitions in a conformationally diverse set of dipeptides have been characterized ab initio using complete active space self-consistent field calculations, and the relevant charge distributions have been parametrized for use in the matrix method for calculations of protein CD. Here, we present calculations of the vacuum UV CD spectra of 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. This significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and the experimental intensity at 175 nm from 0.12 to 0.79. The influence of the conformation on charge-transfer transitions is analyzed in detail, showing that the n --> pi* charge-transfer transitions are most important in alpha-helical proteins, whereas in beta strand proteins the pi --> pi* charge-transfer transition along the chain in the amino- to carboxy-end direction is most dominant.

Simulation study of chiral two-dimensional ultraviolet spectroscopy of the protein backbone.

Amide n-pi* and pi-pi* excitations around 200 nm are prominent spectroscopic signatures of the protein backbone, which are routinely used in ultraviolet (UV) circular dichroism for structure characterization. Recently developed ultrafast laser sources may be used to extend these studies to two dimensions. We apply a new algorithm for modeling protein electronic transitions to simulate two-dimensional UV photon echo signals in this regime and to identify signatures of protein backbone secondary (and tertiary) structure. Simulated signals for a set of globular and fibrillar proteins and their specific regions reveal characteristic patterns of helical and sheet secondary structures. We investigate how these patterns vary and converge with the size of the structural motif. Specific chiral polarization configurations of the UV pulses are found to be sensitive to aspects of the protein structure. This information significantly augments that available from linear circular dichroism.