Using Empirical Phase Diagrams to Understand the Role of Intramolecular Dynamics in Immunoglobulin G Stability

Understanding the relationship between protein dynamics and stability is of paramount importance to the fields of biology and pharmaceutics. Clarifying this relationship is complicated by the large amount of experimental data that must be generated and analyzed if motions that exist over the wide range of timescales are to be included. To address this issue, we propose an approach that utilizes a multidimensional vector-based empirical phase diagram (EPD) to analyze a set of dynamic results acquired across a temperature-pH perturbation plane. This approach is applied to a humanized immunoglobulin G1 (IgG1), a protein of major biological and pharmaceutical importance whose dynamic nature is linked to its multiple biological roles. Static and dynamic measurements are used to characterize the IgG and to construct both static and dynamic empirical phase diagrams. Between pH 5 and 8, a single, pH-dependent transition is observed that corresponds to thermal unfolding of the IgG. Under more acidic conditions, evidence exists for the formation of a more compact, aggregation resistant state of the immunoglobulin, known as A-form. The dynamics-based EPD presents a considerably more detailed pattern of apparent phase transitions over the temperature-pH plane. The utility and potential applications of this approach are discussed

The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation

Background: The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B. Methodology/Principal Findings: As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212-216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers. Conclusions/Significance: Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation. © 2011 Dao et al

Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics

Ancestral sequence reconstruction is a powerful method for inferring ancestors of modern enzymes and for studying structure-function relationships of enzymes. We have previously applied this approach to haloalkane dehalogenases (HLDs) from the subfamily HLD-II and obtained thermodynamically highly stabilized enzymes (Delta T-m up to 24 degrees C), showing improved catalytic properties. Here we combined crystallographic structural analysis and computational molecular dynamics simulations to gain insight into the mechanisms by which ancestral HLDs became more robust enzymes with novel catalytic properties. Reconstructed ancestors exhibited similar structure topology as their descendants with the exception of a few loop deviations. Strikingly, molecular dynamics simulations revealed restricted conformational dynamics of ancestral enzymes, which prefer a single state, in contrast to modern enzymes adopting two different conformational states. The restricted dynamics can potentially be linked to their exceptional stabilization. The study provides molecular insights into protein stabilization due to ancestral sequence reconstruction, which is becoming a widely used approach for obtaining robust protein catalysts

Small Molecule Inhibited Parathyroid Hormone Mediated cAMP Response by N–Terminal Peptide Binding

Ligand binding to certain classes of G protein coupled receptors (GPCRs) stimulates the rapid synthesis of cAMP through G protein. Human parathyroid hormone (PTH), a member of class B GPCRs, binds to its receptor via its N–terminal domain, thereby activating the pathway to this secondary messenger inside cells. Presently, GPCRs are the target of many pharmaceuticals however, these drugs target only a small fraction of structurally known GPCRs (about 10%). Coordination complexes are gaining interest due to their wide applications in the medicinal field. In the present studies we explored the potential of a coordination complex of Zn(II) and anthracenyl–terpyridine as a modulator of the parathyroid hormone response. Preferential interactions at the N–terminal domain of the peptide hormone were manifested by suppressed cAMP generation inside the cells. These observations contribute a regulatory component to the current GPCR–cAMP paradigm, where not the receptor itself, but the activating hormone is a target. To our knowledge, this is the first report about a coordination complex modulating GPCR activity at the level of deactivating its agonist. Developing such molecules might help in the control of pathogenic PTH function such as hyperparathyroidism, where control of excess hormonal activity is essentially required

Analysis and Prediction of the Metabolic Stability of Proteins Based on Their Sequential Features, Subcellular Locations and Interaction Networks

The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions. Determination of protein's metabolic stability would provide us with useful information for in-depth understanding of the dynamic action mechanisms of proteins. Although several experimental methods have been developed to measure protein's metabolic stability, they are time-consuming and more expensive. Reported in this paper is a computational method, which is featured by (1) integrating various properties of proteins, such as biochemical and physicochemical properties, subcellular locations, network properties and protein complex property, (2) using the mRMR (Maximum Relevance & Minimum Redundancy) principle and the IFS (Incremental Feature Selection) procedure to optimize the prediction engine, and (3) being able to identify proteins among the four types: “short”, “medium”, “long”, and “extra-long” half-life spans. It was revealed through our analysis that the following seven characters played major roles in determining the stability of proteins: (1) KEGG enrichment scores of the protein and its neighbors in network, (2) subcellular locations, (3) polarity, (4) amino acids composition, (5) hydrophobicity, (6) secondary structure propensity, and (7) the number of protein complexes the protein involved. It was observed that there was an intriguing correlation between the predicted metabolic stability of some proteins and the real half-life of the drugs designed to target them. These findings might provide useful insights for designing protein-stability-relevant drugs. The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age

Synthetic glycopolymers as modulators of protein aggregation: influence of chemical composition, topology and concentration

Novel drug excipients are required to achieve stable formulations of protein drug candidates. Synthetic glycopolymers have been shown in some cases to improve protein formulation stability, although their structure function relationship remains unknown. Here we report the synthesis of linear or 4-arm star glycopolymers with different molecular topology and chemical composition, with mannose, galactose, arabinose, N-acetyl glucosamine, lactose and trehalose pendant units - and investigate their modulation of conformational stability and aggregation propensity of a model monoclonal antibody (mAb1). Mono-and di-saccharides with free reducing ends are not frequently utilised as protein stabilisers, due to potential reactivity with a protein’s amine groups. In this study this was circumvented through the use of a stable acetal linker connecting the polymer backbone to the sugar pendant residues, which made the latter virtually non-reactive with amines. The general destabilisation the antibody was determined as anunfolding transition temperature (Tm) of CH2 and Fab structural domains, and aggregation temperature (Tagg). The most prominent effect of the glycopolymers on a temperature induced stress in a low concentration solutions was a decrease in Tm and Tagg, regardless of sugar composition or glycopolymer topology - in contrast to the stabilising effect of the corresponding mono- and di-saccharide constituents. The exceptions of linear-lactose and star-trehalose glycopolymers, which increased Tm of the mAb Fab region and Tagg, however, highlights a more complex structure-function relationship. Accelerated stability studies of the high concentrated mAb solutions (50 mg mL-1) revealed that the increased glycopolymer concentrations generally decreased the mAb stability, as judged by the amount of mAb1 ‘monomer’ molecules in solution, with star- and linear-trehalose glycopolymers further generating visible aggregates. Interestingly the latter effect could not have been predicted from the Tm or Tagg experiments conducted at a low concentration regime. Taken together, the data demonstrate a complex interplay of sugar chemistry and molecular topology of the synthetic glycopolymers on their modulation of protein conformational stability and aggregation propensity. Solution concentration was also an important parameter contributing to the stability modulation, and suggests that the stabilising properties of a sugar as the mono- or di-saccharide cannot be extrapolated to the corresponding glycopolymers

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery. We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We show how, for binding, conformational ensembles provide a way of distinguishing the competing models of induced fit and conformational selection. For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur. Finally, we discuss the limitations of conformational ensembles and highlight some potential applications for the future

The process of considering school consolidation: A qualitative case study

The purpose of this qualitative case study was to explore the values and beliefs of a small select group of Scottsbluff and Gering, Nebraska residents regarding consolidation of their two school districts. The focus of the study was on the complexities of the issue of consolidation for the participants. To set the backdrop for the discussion about consolidation, they described their early years including their family\u27s influence about education, their own K-12 school experiences in Gering and Scottsbluff, the rivalry that had existed over time between the two towns, and their own commitment to community. The study delved into the participants\u27 views on the advantages and disadvantages of consolidation, its potential impact on community, and its influence on students. Change was explored: how resistance to any change was seen as a blocker, how future community crises would impact the receptivity to consolidation; what process for consolidating the schools should be followed; and what leadership would be required to convince the community to support consolidation. The information gained from this study pointed to the importance of considering the more human, emotional issues related to the controversial subject of consolidation of two school districts. The overall community identity and the relationship with schools were closely intertwined. The participants in the research talked about their financial and economic concerns for the future, the current curriculum and programs offered by the public schools, and how community and students might be impacted by a consolidation attempt. The researcher concluded that the logical, rational arguments that might have otherwise sold a consolidation plan may not have been enough to convince residents who had a strong emotional attachment to their schools. Many Gering, Nebraska residents felt their community was unique and wished to preserve its individuality. A proposal to consolidate schools with Scottsbluff would need to address the community\u27s concerns about losing its identity. Other more specific steps to consolidation were recommended by the researcher. The technical merger of Scottsbluff and Gering schools would require extensive study of how to logistically combine two governing boards, staff, administration, facilities, and curricula. The researcher expanded on a few key components of marketing and ultimately selling a consolidation plan to the two communities\u27 residents