Differential Structural Stability Research Articles

Differential thermal stability, conformational stability and unfolding behavior of Eis proteins from Mycobacterium smegmatis and Mycobacterium tuberculosis.

Eis (Enhanced Intracellular Survival) is an important aminoglycoside N-acetyltransferase enzyme contributing to kanamycin resistance in Mtb clinical isolates. Eis proteins from M. tuberculosis (RvEis) and M. smegmatis (MsEis) have 58% identical and 69% similar amino acid sequences and acetylate aminoglycosides at multiple amines. Both the Eis proteins are hexameric and composed of two symmetric trimers. RvEis has remarkable structural stability and heat-stable aminoglycoside acetyltransferase activity. Although the structure and biochemical properties of MsEis have been studied earlier, the detailed characterization of its acetyltransferase activity and structural stability is lacking. In this study, we have performed comparative analysis of structural stability and aminoglycoside acetyltransferase activity of RvEis and MsEis proteins. Unlike RvEis, MsEis undergoes a three-state unfolding induced by heat or chemical denaturants and involves self-association of partially unfolded oligomers to form high molecular weight soluble aggregates. MsEis is highly susceptible to chemical denaturants and unfolds completely at lower concentrations of GdmCl and urea when compared to RvEis. In contrast to RvEis, the oligomeric forms of MsEis are SDS sensitive. However, SDS treatment resulted in increased helix formation in MsEis than RvEis. MsEis shows lesser thermostable activity with a decreased efficiency of kanamycin acetylation in comparison to RvEis. Furthermore, overexpression of MsEis does not provide thermal resistance to M. smegmatis unlike RvEis. Collectively, this study reveals that homologous proteins from pathogenic and nonpathogenic mycobacteria follow different modes of unfolding and demonstrate differential structural stability and activity despite highly similar sequences and oligomeric organization.

Unraveling the differential structural stability and dynamics features of T7 endolysin partially folded conformations

BackgroundCharacterization of partially collapsed protein conformations at atomic level is a daunting task due to their inherent flexibility and conformational heterogeneity. T7 bacteriophage endolysin (T7L) is a single-domain amidase that facilitates the lysis of Gram-negative bacteria. T7L exhibits a pH-dependent structural transition from native state to partially folded (PF) conformation. In the pH range 5–3, T7L PF states display differential ANS binding characteristics. MethodsCD, fluorescence, NMR spectroscopy and lysis assays were used to investigate the structure-stability- dynamics relationships of T7L PF conformations. ResultsStructural studies indicated a partial loss of secondary/tertiary structures compared to its native state. The loss in the tertiary structure and the hydrophobic core opening increases upon decrease of pH from 5 to 3. Thermal denaturation experiments delineated that the pH 5 conformation is thermally irreversible in contrast to pH 3, depicting that hydrophobic core opening is essential for thermal reversibility. Further, urea dependent unfolding features of PF state at pH 5 and 4 evidenced for a collapsed conformation at intermediate urea concentrations. Residue level studies revealed that α1-helix and β3-β4 segment of T7L are the major contributors for such a structural collapse and inherent dynamics. ConclusionsThe results suggested that the low pH PF states of T7L are heterogeneous and exhibits differential structural, unfolding, thermal reversibility, and dynamic features. General significanceUnraveling the structure-stability characteristics of different endolysin conformations is essential for designing novel chimeric and engineered phage endolysins as broadband antimicrobial agents over a varied pH range.

Some Structural Aspects of Language Are More Stable than Others: A Comparison of Seven Methods

Understanding the patterns and causes of differential structural stability is an area of major interest for the study of language change and evolution. It is still debated whether structural features have intrinsic stabilities across language families and geographic areas, or if the processes governing their rate of change are completely dependent upon the specific context of a given language or language family. We conducted an extensive literature review and selected seven different approaches to conceptualising and estimating the stability of structural linguistic features, aiming at comparing them using the same dataset, the World Atlas of Language Structures. We found that, despite profound conceptual and empirical differences between these methods, they tend to agree in classifying some structural linguistic features as being more stable than others. This suggests that there are intrinsic properties of such structural features influencing their stability across methods, language families and geographic areas. This finding is a major step towards understanding the nature of structural linguistic features and their interaction with idiosyncratic, lineage- and area-specific factors during language change and evolution.

Comparison of activity and conformational changes of ficin during denaturation by urea and guanidine hydrochloride

The activity and conformational changes of ficin (EC 3.4.22.3), a cysteine protease from Ficus carica have been investigated during the denaturation by urea and guanidine hydrochloride (GuHCl). The denaturation of ficin was followed by activity measurements, fluorescence and circular dichroism (CD) spectroscopic studies. The enzyme activity decreased significantly at low concentration of both urea and GuHCl before unfolding of the enzyme molecule. The enzyme molecule was resistant for unfolding by urea under neutral conditions even at higher concentrations. However, the protein is susceptible to unfolding by urea at lower pH and transition follows a cooperative two-state rule with increasing concentration of urea. On the other hand, ficin molecule loses its complete structure in presence of 4M GuHCl under neutral conditions. The GuHCl-induced unfolding occurs in a simple two-state cooperative process. These results indicate the differential structural stability and fragility of active site of the enzyme towards denaturation by urea and GuHCl.

Structural stability can shape biological evolution

We analyze a model of biological evolution recently introduced in the literature and show that punctuated equilibrium and power-law behavior arise because of the differential structural stability of the mapping between genotype and phenotype that characterizes the model. Structural stability is a feature of biological organisms that had been introduced by biologists long ago, but never modelled until now, as far as we know. This model can be regarded as an alternative to those models that explain both the power-law behavior and the punctuated equilibrium of extinction curves by recourse to self-organized criticality (SOC).

Fluctuations in molecular size, entanglement complexity, and anisometry along molecular dynamics trajectories of short α‐helices

AbstractWe present a detailed study of the intrinsic shape stability of short flexible polypeptide chains by using a number of distinct descriptors. Some large‐scale structural features found in macromolecular folding—unfolding dynamics can be monitored in terms of molecular size and compactness. Similarly, one could employ descriptors of anisometry to that purpose. In addition, we have recently proposed a new family of global, absolute shape descriptors to quantify the complexity of the self‐entanglements in a polymer, or, loosely, its “degree of folding.” This latter aspect of the molecular shape is characterized by combining simple geometrical and topological properties of the α‐carbon backbone. The resulting descriptor, the probability of observing a rigid backbone as a projected curve exhibiting N overcrossings, has been employed already for the analysis of molecular dynamics of linear hydrocarbons and aliphatic carboxylic acids. In this work, three distinct properties of a molecular chain are monitored simultaneously, for the first lime, along computer‐simulated dynamic trajectories: size, anisotropy, and entanglements. The systems studied are a series of 3 polypeptide helices: 10‐polyalanine, 10‐polyvaline, and 10‐polyglycine. Constant temperature trajectories have been computed for these helices, at thermal equilibrium with a simulated external bath, with temperatures ranging from 300 to 700 K. The differential structural stability of the helices is assessed from the various viewpoints. Even though the systems are simple, they contain some of the essential features expected in polypeptides of relevance to structural biology. The results show that the, descriptors of anisometry and entanglements are rather independent. For instance, it is found that, contrary to intuition the unfolding of helices may involve nonhelical “coil” configurations that are both self‐entangled and prolate. The simultaneous study of independent shape descriptors provides a new picture of the nature of conformations found during dynamics trajectories. The resulting description characterizes a polymer conformation in a absolute terms, and not relative to an ad hoc reference structure. The proposed approach gives some insights into the stability of secondary structural motifs in proteins and the mechanisms involved into their formation or unfolding. © 1995 John Wiley & Sons, Inc.

Global characterization of protein secondary structures. Analysis of computer-modeled protein unfolding

Analyses of structural and molecular shape changes undergone by a protein during an unfolding process are presented. The procedure, based on a spherical shape map method, provides a topological description of a three-dimensional macromolecular structure. Local properties of the backbone are used to derive a global characterization of its fold. A spherical shape map of backbone crossings is associated with a given macromolecular conformation. The map is built by classifying each point on the sphere according to the crossing pattern obtained when the backbone is observed along a direction defined by the center of the sphere and the chosen point. The surface of the sphere can be divided in equivalence classes. All the points within a given class correspond to directions from which the back-bone has the same overcrossing pattern. Automatic computation and display of these equivalence classes is discussed, as is the implementation of the technique on a computer graphics workstation. The graphical manipulation simplifies the analysis of these maps when following a change in the conformation of the backbone. The procedure is illustrated with the results of a molecular dynamics computer simulation of the unfolding of the bacteriophage T4 glutaredoxin protein (in the form of its polyglycine model). The method gives a novel description of the differential structural stability for the characteristic secondary structural elements (α-helices and β-sheets) present in the protein. Recognition of the persistence of structural elements over the simulation time is performed in an unbiased manner.

Structural behavior of fracture zones symmetric and asymmetric about a spreading axis: Mid-Atlantic Ridge (latitude 23°N to 27°N)

Two classes of fracture zones are distinguished on the basis of their orientations with respect to a spreading axis and length of associated ridge-ridge transform offset. (1) Minor fracture zones associated with transform faults of short offset ( 50 km); the major fracture zones exhibit a symmetric configuration with respect to a spreading axis following small circles about poles of plate rotation. Recognition of the coexistence of the two classes of fracture zones with different orientations on a slow-spreading oceanic ridge raises questions regarding the significance of the different orientations and nature of the intervening structural transition. A systematic narrow-beam bathymetric and magnetic investigation was performed to answer these questions in an area encompassing the change from minor fracture zones asymmetric with respect to the axis of the rift valley of the Mid-Atlantic Ridge at lat 26°N between major fracture zones, and a major fracture zone, the Kane, symmetric with respect to the axis of the rift valley at lat 24°N. The investigation delineated an intervening transitional region where structural features have continuously undergone geometric adjustments that have accommodated the discrepancy in orientation between the two classes of fracture zones for at least the past 6 m.y. A hypothesis of differential structural stability determined by thickness of lithosphere within transform offsets is advanced to explain the observed differences in behavior of the two classes of fracture zones. The orientation of a major fracture zone is constrained to follow small circles along a trajectory of relative plate motion by a long section of thick lithosphere in the associated transform fault. The orientation of a minor fracture zone is susceptible to reorientation in the short section of thin lithosphere in the associated transform fault; the reorientation reflects response to intra-plate and interplate stresses. The geometric adjustments that occur as a consequence of differential structural stability continuously accommodate any discrepancy in orientation that may develop between coexistent major and minor fracture zones, so that an ocean basin such as the Atlantic can open symmetrically.