On a geometry-based approach to protein sequence alignment

We consider a novel numerical representation of proteins obtained by assigning to individual amino acids the polar coordinate on a unit circle. As a result one can represent protein sequence as one-dimensional numerical sequence, the entries of which when subtracted facilitates search for alignment between pairs of proteins of interest. The alignment is sought by shifting one sequence relative to another by several sequence units to the left or to the right. The novel approach is illustrated on two yeast proteins having 174 and 171 amino acids. Visiting Emeritus from the Department of Mathematics & Computer Science Drake University, Des Moines, Iowa.     

Periodic force induced stabilization or destabilization of the denatured state of a protein

We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time starts increasing as the noise-induced hoping event (from the denatured state to the native state) begins to experience many oscillations over the mean barrier crossing time period. Thus unlike one-dimensional barrier crossing problems, the external oscillating force field induces both stabilization or destabilization of the denatured state of a protein. We have also studied the parametric dependence of the folding dynamics on temperature, viscosity, non-Markovian character of bath in presence of the external field.     

Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm

In this article, we describe a representation for the processes of multiple sequences alignment (MSA) and used it to solve the problem of MSA. By this representation, we took every possible aligning result into account by defining the representation of gap insertion, the value of heuristic information in every optional path and scoring rule. On the basis of the proposed multidimensional graph, we used the ant colony algorithm to find the better path that denotes a better aligning result. In our article, we proposed the instance of three‐dimensional graph and four‐dimensional graph and advanced a special ichnographic representation to analyze MSA. It is yet only an experimental software, and we gave an example for finding the best aligning result by three‐dimensional graph and ant colony algorithm. Experimental results show that our method can improve the solution quality on MSA benchmarks. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Magnetizability tensors from auxiliary density functional theory

The working equations for the calculation of the magnetizability tensor in the framework of auxiliary density functional theory with gauge including atomic orbitals (ADFT-GIAO) are derived. Unlike in the corresponding conventional density functional theory implementations the numerical integration of the GIAOs is avoided in ADFT-GIAO. Our validation shows that this simplification has no effect on the accuracy of the methodology. As a result, a reliable and efficient implementation for the calculation of magnetizabilities of systems with more than 1000 atoms and 14 000 basis functions is presented.     

StructSorter: a method for continuously updating a comprehensive protein structure alignment database

Advances in protein crystallography and homology modeling techniques are producing vast amounts of high resolution protein structure data at ever increasing rates. As such, the ability to quickly and easily extract structural similarities is a key tool in discovering important functional relationships. We report on an approach for creating and maintaining a database of pairwise structure alignments for a comprehensive database comprising the PDB and homology models for the human and select pathogen genomes. Our approach consists of a novel, multistage method for determining pairwise structural similarity coupled with an efficient clustering protocol that approximates a full NxN assessment in a fraction of the time. Since biologists are commonly interested in recently released structures, and the homology models built from them, an automatically updating database of structural alignments has great value. Our approach yields a querying system that allows scientists to retrieve databank-wide protein structure similarities as easily as retrieving protein sequence similarities via BLAST or PSI-BLAST. Basic, noncommercial access to the database can be requested at https://tip.eidogen-sertanty.com/.     

Electronically activated actin protein polymerization and alignment

Biological systems are the paragon of dynamic self-assembly, using a combination of spatially localized protein complexation, ion concentration, and protein modification to coordinate a diverse set of self-assembling components. Biomimetic materials based upon biologically inspired design principles or biological components have had some success at replicating these traits, but have difficulty capturing the dynamic aspects and diversity of biological self-assembly. Here, we demonstrate that the polymerization of ion-sensitive proteins can be dynamically regulated using electronically enhanced ion mixing and monomer concentration. Initially, the global activity of the cytoskeletal protein actin is inhibited using a low-ionic strength buffer that minimizes ion complexation and protein-protein interactions. Nucleation and growth of actin filaments are then triggered by a low-frequency AC voltage, which causes local enhancement of the actin monomer concentration and mixing with Mg(2+). The location and extent of polymerization are governed by the voltage and frequency, producing highly ordered structures unprecedented in bulk experiments. Polymerization rate and filament orientation could be independently controlled using a combination of low-frequency (approximately 100 Hz) and high frequency (1 MHz) AC voltages, creating a range of macromolecular architectures from network hydrogel microparticles to highly aligned arrays of actin filaments with approximately 750 nm periodicity. Since a wide range of proteins are activated upon complexation with charged species, this approach may be generally applicable to a variety of biopolymers and proteins.     

Calculation of intramolecular force fields from second-derivative tensors

A practical procedure (FUERZA) to obtain internal force constants from Cartesian second derivatives (Hessians) is presented and discussed. It allows a systematic analysis of pair atomic interactions in a molecular system, and it is fully invariant to the choice of internal coordinates of the molecule. Force constants for bonds or for any pair of atoms in general are defined by means of the eigenanalysis of their pair interaction matrix. Force constants for the angles are obtained from their corresponding two-pair interaction matrices of the two bonds or distances forming the angle, and the dihedral force constants are similarly obtained using their corresponding three-pair interaction matrices. © 1996 John Wiley & Sons, Inc.     

SDS-induced multi-stage unfolding of a small globular protein through different denatured states revealed by single-molecule fluorescence

Ionic surfactants such as sodium dodecyl sulfate (SDS) unfold proteins in a much more diverse yet effective way than chemical denaturants such as guanidium chloride (GdmCl). But how these unfolding processes compare on a molecular level is poorly understood. Here, we address this question by scrutinising the unfolding pathway of the globular protein S6 in SDS and GdmCl with single-molecule Förster resonance energy transfer (smFRET) spectroscopy. We show that the unfolding mechanism in SDS is strikingly different and convoluted in comparison to denaturation in GdmCl. In contrast to the reversible two-state unfolding behaviour in GdmCl characterised by kinetics on the timescale of seconds, SDS demonstrated not one, but four distinct regimes of interactions with S6, dependent on the surfactant concentration. At ≤1 mM SDS, S6 and surfactant molecules form quasi-micelles on a minute timescale; at millimolar [SDS], the protein denatures through an unfolded/denatured ensemble of highly heterogeneous states on a multi-second timescale; at tens of millimolar of SDS, the protein unfolds into a micelle-packed conformation on the second timescale; and >50 mM SDS, the protein unfolds with millisecond timescale dynamics. We propose a detailed model for multi-stage unfolding of S6 in SDS, which involves at least three different types of denatured states with different level of compactness and dynamics and a continually changing landscape of interactions between protein and surfactant. Our results highlight the great potential of single-molecule fluorescence as a direct probe of nanoscale protein structure and dynamics in chemically complex surfactant environments.

Multi-stage unfolding of S6 in SDS involving various types of denatured states with different levels of compactness and dynamics.     

NMR shielding tensors from auxiliary density functional theory

The working equations for the calculation of NMR shielding tensors in the framework of auxiliary density functional theory are derived. It is shown that in this approach the numerical integration over gauge-including atomic orbitals can be avoided without the loss of accuracy. New integral recurrence relations for the required analytic electric-field-type integrals are derived. The computational performance of the resulting formalism permits shielding tensor calculations of systems with more than 1000 atoms and 15,000 basis functions.     

A thermochemiluminescence array for recognition of protein subtypes and their denatured shapes

Thermochemiluminescence (TCL) of organic compounds or biological substances is an interesting phenomenon and has been applied to polymer analysis and medical diagnostics. We improve traditional TCL assays using the assistance of catalytic nanomaterials and construct a nanomaterials array for the discrimination of three subtypes of proteins (albumin from human serum, bovine serum and porcine serum). With the assistance of catalytic nanomaterials, TCL signals of different protein samples are distinct due to the diverse catalytic activities of the nanomaterials and characteristics of proteins. Using this array-based technology, we obtained unique TCL patterns as 'fingerprints', and then accurately classified these 3 subtypes of serum albumins and the denatured albumins under different heat conditions. In the blind test, 24 unknown samples randomly chosen from these albumins were all assigned to the accurate groups. Moreover, on several nanomaterials, the intensity of TCL could be greatly amplified. For example, on MgO and BaO, albumins in aqueous solutions at 2 μg mL(-1) (~30 nM) offered robust responses. This improved TCL assay with reversible response and simple instrumentation can offer high differentiability and sensitivity.     

Antibodies to short synthetic peptides for specific recognition of partly denatured protein

On immunization with subclasses of homologous proteins, the presence of immunodominant class-specific structures often prevents the development of subclass specific antibodies. Immunization with synthetic peptides representing specific structures in such a protein can then be used instead. Sequences derived from human IgG2 and Staphylococcus aureus enterotoxin were used as a model to develop general criteria for immunization with synthetic peptides. Peptide sequences were selected on the basis of criteria such as hydrophilic property, surface probability and secondary structure, which together constitute an antigenic index. The carrier proteins keyhole limpet hemocyanin and chicken gammaglobulin were coupled by using either carbodiimide or a maleimide. Peptide-specific responses can be elicited regardless of the sequence. Some coupling conditions influenced the specificity of the antibody responses. The results of immunization with short peptides not representing a natural B-cell determinant of a protein suggest that the frequency of native protein-recognizing antibodies is considerably lower than that of antibodies that recognize the protein in a partly denatured or altered state.     

Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovine acyl-coenzyme A binding protein (ACBP) at three different concentrations of guanidine hydrochloride. As the experimentally determined distance information corresponds to weighted averages over a broad ensemble of structures, we applied the experimental restraints to a system of noninteracting replicas of the protein by using a Monte Carlo sampling scheme. This procedure permits us to sample ensembles of conformations that are compatible with the experimental data and thus to obtain information regarding the distribution of structures in the denatured state. Our results show that the denatured state of ACBP is highly heterogeneous. The high sensitivity of the computational method that we present, however, enabled us to identify long-range interactions between two regions, located near the N- and C-termini, that include both native and non-native elements. The preferential formation of these contacts suggests that the sequence-dependent patterns of helical propensity and hydrophobicity are important determinants of the structure in the denatured state of ACBP.     

QM/MM calculation of protein magnetic shielding tensors with generalized hybrid-orbital method: a GIAO approach

A method to compute magnetic shielding tensors with generalized hybrid-orbital (GHO) QM/MM scheme is developed at the levels of Hartree-Fock and second-order M?ller-Plesset perturbation theory using gauge-including atomic orbitals. A feature of the GHO method is utilized to ensure gauge-origin independency of GHO shielding tensors in a simple way. The benchmark calculations indicate that the GHO method reproduced full-QM shielding constants nearly quantitatively for atoms not directly coupled to the GHO linking atoms. As an application to a realistic protein, carbon chemical shifts are calculated for the retinal chromophore in visual rhodopsin.     

Multiple flexible alignment with SEAL: a study of molecules acting on the colchicine binding site

An extension of the steric and electrostatic alignment alignment (SEAL) method (MultiSEAL) is described that allows the overlay of multiple molecules and conformations. The method is well-suited for the systematic study of possible alignments, also revealing information about the conformational energies associated with a given overlay. It has been tested on three examples: angiotensin II antagonists, 5-HT3 antagonists, and dopaminergic compounds. The utility of the method is further demonstrated in an analysis of molecules that putatively bind to the colchicine site of tubulin. On the basis of its overlay with colchicine, allocolchicine, 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone, and combretastatin A-4, it appears that 2-methoxyestradiol (2-ME) is unlikely to fit the colchine site properly. The weak antimitotic activity of 2-ME may be explained by its partial fit in the site.     

Residual native structure in a thermally denatured beta-hairpin

We investigate the thermal denaturation of trpzip2 between 15 and 82 degrees C using two-dimensional infrared (2D IR) vibrational spectroscopy, dispersed vibrational echo (DVE) spectroscopy, and Fourier transform infrared (FTIR) spectroscopy. The FTIR and DVE spectra of trpzip2 show in the amide I region of the spectrum two resonances, which arise primarily from the interstrand coupling between local amide I oscillators along the peptide backbone. The coupling is seen directly in the 2D IR spectra as the formation of cross-peak ridges. Although small shifts of these frequencies occur on heating the sample, the existence of cross-peak ridges at all temperatures indicates that stable hydrogen bond interactions persist between the two beta-strands. These observations indicate a significant amount of native structure in the thermally denatured state of trpzip2.     

Effect of salt concentrations on the displacement adsorption enthalpies of denatured protein folding at a moderately hydrophobic surface

Lead(II) complexes of reduced glutathione (GSH) of general composition [Pb(L)(X)]·H₂O (where L=GSH; X=Cl, NO₃, CH₃COO, NCS) have been synthesized and characterized by elemental analyses, infrared spectra and electronic spectra. Thermogravimetric (TG) and differential thermal analytical (DTA) studies have been carried out for these complexes. Infrared spectra indicate deprotonation and coordination of cysteinyl sulphur with metal ion. It indicates the presence of water molecule in the complexes that has been supported by TG/DTA. The thermal behaviour of complexes shows that water molecule is removed in first step-followed removal of anions and then decomposition of the ligand molecule in the subsequent steps. Thermal decomposition of all the complexes proceeds via first order kinetics. The thermodynamic activation parameters, such as E*, A, ΔH*, ΔS* and ΔG* have been calculated. The geometry of the metal complexes has been studied with the help of molecular modeling for energy minimization calculation.     

Integrating protein secondary structure prediction and multiple sequence alignment

Modern protein secondary structure prediction methods are based on exploiting evolutionary information contained in multiple sequence alignments. Critical steps in the secondary structure prediction process are (i) the selection of a set of sequences that are homologous to a given query sequence, (ii) the choice of the multiple sequence alignment method, and (iii) the choice of the secondary structure prediction method. Because of the close relationship between these three steps and their critical influence on the prediction results, secondary structure prediction has received increased attention from the bioinformatics community over the last few years. In this treatise, we discuss recent developments in computational methods for protein secondary structure prediction and multiple sequence alignment, focus on the integration of these methods, and provide some recommendations for state-of-the-art secondary structure prediction in practice.