The Critical Role Of Conformational Flexibility In The Toxin Life Cycle

Bacterial protein toxins are typically produced as water-soluble proteins. However, many of these toxins exert at least some of their effects at the target membrane. These proteins must therefore possess characteristics of both water-soluble and membrane proteins. It then follows that these proteins are often required to undergo large conformational changes in order to exert their toxic mode of action. Understanding the energetics and molecular details of these conformational changes is critical to elucidating the mode of action of protein toxins, with the goals of improving toxin activities (as in the cases of Bt toxins applied to crop biotechnology or immunotoxin improvement for disease therapies), or inhibiting toxin activities (as in the cases of disease management or bioterrorism prevention). In the following sections, we will briefly introduce methods for studying protein conformational changes, followed by a section on factors contributing to the stabilization of protein structures. These introductory sections will then be followed by discussions on soluble protein folding, membrane protein folding, and finally an integration of these two models into a model for understanding bacterial protein toxin conformational changes.

2.2.1 Studying Protein Conformational Changes

In a perfect scenario for studying the conformational changes of a protein, the three-dimensional structure of each of the relevant states is known. However, in the real world, this is rarely the case. For many proteins, the detailed structure of the native


Central Questions in Protein Toxin Research, Organized by Toxin Life Stage with Toxin Examples3

Central Question or Theme w


Bordetella pertussis adenylate cyclase toxin1

a-bungaro toxin2

Chlamydia CADD3



Life Stage

Cell recognition

Cell recognition

Terminal toxic event

Proteolytic Stability



Tertiary structure

Ca-dependent quaternary structure


Change triggers

Redox trigger

Toxin-Receptor Interaction

Toxin-lipid interaction

Toxin-ACh receptor

Secondary Localization Modification


Ca-dependent membrane insertion

Toxin Class

Repeats in Toxin Family (RTX)

ACh receptor binding

Tumor necrosis factor binding

Pore-forming toxin

Toxic Event

Cell leakage


Apoptosis activation

Membrane leakage

Membrane leakage

Colicin E96

N-terminal Tertiary domain stability assignment

Tol B interaction site

Translocation signal domain

DNA hydrolysis

DNA hydrolysis i ot e n

H. pylori vacuolating toxin VacA7-11

Solution structure, localization7 Terminal toxic action11


Structural alteration, localization

Variable oligomeric morphology7 Secondary structure-function assignment11 Quaternary structure determinants11

Acid activation7

Acid activation domains11

Lipid-induced conformational change

Yeast K1 viral Cell recognition9 toxin9-13

Clostridium difficile toxin B10

Cell recognition

E. coli cytotoxic necrotizing factor l12

Vibrio cholerae toxin14

Solution structure, terminal toxic event12

Tertiary structure

Numbers refer to chapter references.

Receptor interaction9,13

Toxin-actin interaction


Membrane leakage

Receptor lossĀ«

A/B toxin, ribosome inactivating toxin

Ion channel activation and pore formation

ADP ribosylation

Disrupted H+ transport

Rho-GTPase Inactivation binding of GTPase protein toxin causing actin depolymeri-

Rho-GTPase toxin zation

Actin polymerization


protein is known from either x-ray crystallographic data or solution proton nuclear magnetic resonance (NMR) experiments. In some cases, structural information from both techniques is known. NMR-derived structural information is richer than x-ray crystal structure data in that the former also yields insights into the conformational dynamics around the equilibrium structure. NMR can also be used to gather information about protein intermediates, either under native state conditions or by manipulating solution conditions to favor a particular state. Although there is a plethora of structural information for proteins in their native states, to date the detailed molecular structure of a denatured protein has yet to be described. This is undoubtedly due to the conformational heterogeneity of the unfolded state, which hampers structure determination via protein crystallography or NMR spectroscopy. Some general features of unfolded proteins have been described using other biophysical tools such as circular dichroism (CD) spectroscopy or hydrogen exchange measured by NMR.

The absence of detailed structural information does not preclude one from gaining important insights into the conformational changes related to protein function. The only requirement for monitoring protein conformation is a measurable property of the protein that is related to one particular protein state. Proteins have a few intrinsic properties that are suitable for just such observation. Protein secondary structure is a useful indicator of protein conformation and can be monitored using CD spec-troscopy. The loss of protein secondary structure is an indication of the transition from a structured protein state to a less-structured unfolded state. These types of structural alterations may play an important role in the mode of action for a given protein toxin. CD spectroscopy reports on the overall protein conformation. Other spectroscopic techniques such as fluorescence or electron paramagnetic resonance (EPR) spectroscopy can be used to gather more site-specific information. However, to get the more detailed site-specific information, specific residues in the protein are labeled with probes, fluorophores, or paramagnetic molecules. Signals from these incorporated probes can then be followed in in vitro assays that follow specific steps in the mode of action such as protein binding, pore formation, etc. Using a variety of biophysical tools allows one to collect a diverse set of complementary data that can be used to identify localized regions of the toxin that play critical roles in the mode of action of the protein.

2.2.2 Forces that Contribute to Protein Stability

Most soluble proteins are marginally stable, typically 3-10 kcal/mol. Therefore, the forces that contribute to stability are balanced delicately near the transition from folded to unfolded protein. The types of interactions that are responsible for protein stability and conformation can be generally classified as hydrophobic or polar, with hydrogen bonding or electrostatic interactions comprising the polar interactions. There is no consensus regarding which of these forces plays the predominant role in protein stability; this has been debated for almost 70 years. Early on, it was suggested that the hydrophobic effect was the primary determinant of protein stability and that hydrogen bonding was at best neutral, or likely destabilizing. In more recent times, hydrogen bonding has come to be viewed as a potentially stabilizing force in maintaining protein structure. Given the marginal stability of proteins in general, it is probably true that for any given protein hydrophobicity may predominate, whereas in a different protein hydrogen bonding may predominate.

Studies on protein stability have led to the general observation that hydrogen bonding can provide more specificity to protein structure than hydrophobic interactions. Mutational studies have shown that proteins are able to slightly adjust local conformation to compensate for changes in hydrophobic packing interactions with marginal effects on protein stability and overall structure. Hydrogen bonds provide specificity due to the directional nature and geometric constraints of a hydrogen bond. Recent studies have shown that a specific side-chain hydrogen bond can provide structural specificity to transmembrane helix interactions.14 In terms of protein toxin mode of action, both hydrophobic and hydrogen bonding interactions can play significant roles in determining the structural interactions that produce the toxic effect on the target site(s) in the cell.

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