Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A.

The B domain of protein A (BdpA), a small three-helix bundle, folds on a time scale of a few microseconds with heterogeneous native and unfolded states. It is widely used as a model for understanding protein folding mechanisms. In this work, we use structure-based models (SBMs) and atomistic simulations to comprehensively investigate how BdpA folding is associated with the formation of its secondary structure. The energy landscape visualization method (ELViM) was used to characterize the pathways that connect the folded and unfolded states of BdpA as well as the sets of structures displaying specific ellipticity patterns. We show that the native state conformational diversity is due mainly to the conformational variability of helix I. Helices I, II, and III occur in a weakly correlated manner, with Spearman's rank correlation coefficients of 0.1539 (I and II), 0.1259 (I and III), and 0.2561 (II and III). These results, therefore, suggest the highest cooperativity between helices II and III. Our results allow the clustering of partially folded structures of folding of the B domain of protein A on the basis of its secondary structure, paving the way to an understanding of environmental factors in the relative stability of the basins of the folding ensemble, which are illustrated by the structural dependency of the protein hydration structures, as computed with minimum-distance distribution functions.

Distinguishing Biomolecular Pathways and Metastable States.

Protein folding occurs in a high dimensional phase space, and the representation of the associated energy landscape is nontrivial. A widely applied approach to studying folding landscapes is to describe the dynamics along a small number of reaction coordinates. However, other strategies involve more elaborate analysis of the complex phase space. There have been many attempts to obtain a more detailed representation of all available conformations for a given system. In this work, we address this problem using a metric based on internal distances between amino acids to describe the differences between any two conformations. Using an effective projection method, we are able to go beyond the typical one-dimensional representation and provide intuitive two dimensional visualizations of the landscape. We refer to this method as the energy landscape visualization method (ELViM). We have applied this methodology using a Cα structure-based model to study the folding of two well-known proteins: SH3 domain and protein-A. Our visualization method yields a detailed description of the folding process, making possible the identification of transition state regions, and establishing the paths that lead to the native state. For SH3, we have analyzed structural differences in the distribution of folding routes. The competition between the native and mirror structures in protein A is also discussed. Finally, the method is applied to study conformational changes in the protein elongation factor thermally unstable. Distinct features of ELViM are that it does not require or assume a reaction coordinate, and it does not require analysis of kinetic aspects of the system.

Protein A chromatography: Challenges and progress in the purification of monoclonal antibodies.

Antibodies for therapeutic use are being continuously approved and their demand has been steadily growing. As known, the golden standard for monoclonal antibody (mAb) purification is Protein A affinity chromatography, a technology that has gained high interest because of its great performance and capabilities. The main concerns are the elevated resins costs and their limited lifetime compared to other resins (e.g. ion exchange chromatography). Great efforts have been carried out to improve purification conditions, such as resin characterization and designing alkali/acid stable resins with a longer lifetime. Modification of Protein A ligands and alternative formats such as monoliths membranes and microshperes have been tested to increase the purification performance. New technology has been proposed to improve the large-scale separation; in addition, alternative ligands have been suggested to capture mAbs instead of Protein A ligand; however, most of the information is locked by pharmaceutical companies. This mini review summarizes and describes the advances, results, and impact on the Protein A chromatography purification processing.

The recombination dynamics of Staphylococcus aureus inferred from spA gene.

BACKGROUND: Given the role of spA as a pivotal virulence factor decisive for Staphylococcus aureus ability to escape from innate and adaptive immune responses, one can consider it as an object subject to adaptive evolution and that variations in spA may uncover pathogenicity variations. RESULTS: The population genetic structure was deduced from the extracellular domains of SpA gene sequence (domains A-E and the X-region) and compared to the MLST-analysis of 41 genetically diverse methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) S. aureus strains. Incongruence between tree topologies was noticeable and in the inferred spA tree most MSSA isolates were clustered in a distinct group. Conversely, the distribution of strains according to their spA-type was not always congruent with the tree inferred from the complete spA gene foreseeing that spA is a mosaic gene composed of different segments exhibiting different evolutionary histories. Evidences of a network-like organization were identified through several conflicting phylogenetic signals and indeed several intragenic recombination events (within subdomains of the gene) were detected within and between CC's of MRSA strains. The alignment of SpA sequences enabled the clustering of several isoforms as a result of non-randomly distributed amino acid variations, located in two clusters of polymorphic sites in domains D to B and Xr (a). Nevertheless, evidences of cluster specific structural arrangements were detected reflecting alterations on specific residues with potential impact on S. aureus pathogenicity. CONCLUSIONS: The detection of positive selection operating on spA combined with frequent non-synonymous mutations, domain duplication and frequent intragenic recombination events represent important mechanisms acting in the evolutionary adaptive mechanism promoting spA genetic plasticity. These findings argue that crucial allelic forms correlated with pathogenicity can be identified by sequences analysis enabling the design of more robust schemes.

Elution relationships to model affinity chromatography using a general rate model.

Different mathematical models with different degrees of complexity have been proposed to model affinity chromatography. In this work, in particular, a general rate model has been studied that considers axial dispersion, external film mass transfer, intraparticle diffusion, and kinetic effects investigating the influence in the simulations of two different relationships between the properties of the mobile phase and the affinity of different proteins to the ligand bound to the matrix. Two systems were used: Blue Sepharose and Protein A. With Blue Sepharose, an increasing linear salt gradient was used, and with Protein A, a decreasing semi-linear pH gradient. The kinetic parameters obtained in each of the two elution (adsorption/desorption) relationships studied (a power law type and an exponential type) led to very good agreements between experimental and simulated elution curves of mixtures of proteins finding that for more symmetrical peaks, the preferred elution relationship should be the exponential one, in contrast to the more asymmetrical peaks which shapes are better simulated by the power law relationship.

Conjugation of colloidal gold to proteins.

The ability to conjugate proteins to colloidal gold sols provides a wide variety of probes for electron microscopy. Antibodies, protein A, protein G, lectins, enzymes, toxins, and other proteins have all been conjugated to colloidal gold. The nature of the interaction between the colloidal gold and the protein is poorly understood. Proteins are conjugated to gold sols by adjusting the pH of the gold sol to approximately 0.5 pH unit higher than the pI of the protein being conjugated. This chapter gives a general method for conjugating proteins to colloidal gold as well as more specific methods for conjugating antibodies and protein A to colloidal gold.

Protein L-agarose for adsorption of autoantibodies: a potential tool for extracorporeal treatment.

This work investigated the adsorption of autoantibodies such as anti-SS-A/Ro, anti-SS-B/La, anti-Sm, and anti-dsDNA on protein L-agarose gel. In order to determine better conditions for IgG adsorption on this matrix, some buffer systems were tested. Adsorption data were analyzed using the Langmuir and Langmuir-Freundlich isotherm models. The experimental isotherms were best described by the Langmuir-Freundlich model, which indicated negative and positive cooperativities for binding in the presence of PBS and HEPES buffers, respectively. The K(d) values for phosphate buffered saline solution (PBS) and hydroxyethylpiperazine ethanesulfonic acid (HEPES) were 2.8 x 10(-7) M and 3.2 x 10(-7) M, respectively, which indicate a high affinity between IgG and the immobilized protein L. The amount of protein adsorbed per amount of protein loaded was high for anti-Sm (44%) and anti-dsDNA (46%), but low for anti-SS-B/La (9%). The amount of albumin adsorbed was lower than 0.06 mg/mL, which may remove the need for a plasma replacement solution in clinical apheresis.

Chromatographic removal combined with heat, acid and chaotropic inactivation of four model viruses.

The virus removal of protein A affinity chromatography, inactivation capacity, acid pH and a combination of high temperature with a chaotropic agent was determined in this work. The model viruses studied were sendaivirus, human immunodeficency virus (HIV-IIIb), human poliovirus type-II, human herpesvirus I and canine parvovirus. The protein A affinity chromatography showed a maximum reduction factor of 8 logs in the case of viruses larger than 120 nm size, while for small viruses (18-30 nm) the maximum reduction factor was about 5 logs. Non viral inactivation was observed during the monoclonal antibody elution step. Low pH treatment showed a maximum inactivation factor of 7.1 logs for enveloped viruses. However, a weak inactivation factor (3.4 logs) was obtained for DNA nonenveloped viruses. The combination of high temperature with 3 M KSCN showed a high inactivation factor for all of the viruses studied. The total clearance factor was 23.1, 15.1, 13.6, 20.0 and 16.0 logs for sendaivirus, HIV-IIIb, human poliovirus type-II, human herpesvirus I and canine parvovirus, respectively.