Correlation between Protein Stability Cores and Protein Folding Kinetics: A Case Study on Pseudomonas aeruginosa Apo-Azurin

The Zero-Order Loop in Apoazurin Modulates Folding Mechanism In Silico

Pseudomonas aeruginosa apoazurin (apo, without the copper cofactor) has a single disulfide bond between residues 3 and 26 and unfolds in a two-state reaction in vitro. The disulfide bond covalently connects the N-termini of β-strands 1 and 3; thereby, it creates a zero-order loop or a "cinch" that restricts conformational space. Covalent loops and threaded topologies are emerging as important structural elements in folded proteins and may be important for function. In order to understand the role of a zero-order loop in the folding process of a protein, here we used coarse-grained molecular dynamics (CGMD) simulations in silico to compare two variants of apoazurin: one named "loop" which contained the disulfide, and another named "open" in which the disulfide bond between residues 3 and 26 was removed. CGMD simulations were performed to probe the stability and unfolding pathway of the two apoazurin variants at different urea concentrations and temperatures. Our results show that the covalent loop plays a prominent role in the unfolding mechanism of apoazurin; its removal alters both the folding-transition state and the unfolded-state ensemble of conformations. We propose that modulation of azurin's folding landscape by the disulfide bridge may be related to both copper capturing and redox sensing.

Folding of copper proteins: role of the metal?

Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein-protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.

A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO)

We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures the covolume of a test protein and a macromolecule against the covolume of a test protein and a sphere of equal volume as that of a macromolecule for the criteria of coarse-graining a cytoplasmic model. A cutoff λ(c) = 0.8 was chosen based on the size of a test protein and computational resources and it determined the resolution of a coarse-grained cytoplasm. We compared the results from a polydisperse cytoplasmic model (PD model) produced by CGCYTO with two other coarse-grained hard-sphere cytoplasmic models: 1), F70 model, macromolecules in the cytoplasm were modeled by homogeneous hard spheres with a radius of 55 Å, the size of Ficoll70 and 2), HS model, each macromolecule in the cytoplasm was modeled by a hard sphere of equal volume. It was found that the folding temperature T(f) of a test protein (apoazurin) in a PD model is ~5° greater than that in a F70 model. In addition, the deviation of T(f) in a PD model is twice as much as that in a HS model when an apoazurin is randomly placed at different voids formed by particle fluctuations in PD models.

Role of metal in folding and stability of copper proteins in vitro

Metal coordination is required for function of many proteins. For biosynthesis of proteins coordinating a metal, the question arises if the metal binds before, during or after folding of the polypeptide. Moreover, when the metal is bound to the protein, how does its coordination affect biophysical properties such as stability and dynamics? Understanding how metals are utilized by proteins in cells on a molecular level requires accurate descriptions of the thermodynamic and kinetic parameters involved in protein-metal complexes. Copper is one of the essential transition metals found in the active sites of many key proteins. To avoid toxicity of free copper ions, living systems have developed elaborate copper-transport systems that involve dedicated proteins that facilitate efficient and specific delivery of copper to target proteins. This review describes in vitro and in silico biophysical work assessing the role of copper in folding and stability of copper-binding proteins. Examples of proteins discussed are: a blue-copper protein (Pseudomonas aeruginosa azurin), members of copper-transport systems (bacterial CopZ, human Atox1 and ATP7B domains) and multi-copper ferroxidases (yeast Fet3p and human ceruloplasmin). The consequences of interactions between copper proteins and platinum-complexes are also discussed. This article is part of a Special Issue entitled: Cell Biology of Metals.

Predicting protein folding cores by empirical potential functions

Theoretical and in vitro experiments suggest that protein folding cores form early in the process of folding, and that proteins may have evolved to optimize both folding speed and native-state stability. In our previous work (Chen et al., Structure, 14 (2006) 1401), we developed a set of empirical potential functions and used them to analyze interaction energies among secondary-structure elements in two beta-sandwich proteins. Our work on this group of proteins demonstrated that the predicted folding core also harbors residues that form native-like interactions early in the folding reaction. In the current work, we have tested our empirical potential functions on structurally-different proteins for which the folding cores have been revealed by protein hydrogen-deuterium exchange experiments. Using a set of 29 unrelated proteins, which have been extensively studied in the literature, we demonstrate that the average prediction result from our method is significantly better than predictions based on other computational methods. Our study is an important step towards the ultimate goal of understanding the correlation between folding cores and native structures.

In vitro unfolding of yeast multicopper oxidase Fet3p variants reveals unique role of each metal site

Fet3p from Saccharomyces cerevisiae is a multicopper oxidase (MCO) that contains 3 cupredoxin-like beta-barrel domains and 4 copper ions located in 3 distinct metal sites (T1 in domain 3, T2, and the binuclear T3 at the interface between domains 1 and 3). To better understand how protein structure and stability is defined by cofactor coordination in MCO proteins, we assessed thermal unfolding of apo and metallated forms of Fet3p by using spectroscopic and calorimetric methods in vitro (pH 7). We find that unfolding reactions of apo and different holo forms of Fet3p are irreversible reactions that depend on the scan rate. The domains in apo-Fet3p unfold sequentially [thermal midpoint (T(m)) of 45 degrees C, 62 degrees C, and 72 degrees C; 1 K/min]. Addition of T3 imposes strain in the apo structure that results in coupled domain unfolding and low stability (T(m) of 50 degrees C; 1 K/min). Further inclusion of T2 (i.e., only T1 absent) increases overall stability by approximately 5 degrees C but unfolding remains coupled in 1 step. Introduction of T1, producing fully-loaded holo-Fet3p (or in the absence of T2), results in stabilization of domain 3, which uncouples unfolding of the domains; unfolding of domain 2 occurs first along with Cu-site perturbations (T(m) 50-55 degrees C; 1 K/min), followed by unfolding of domains 1 and 3 ( approximately 65-70 degrees C; 1 K/min). Our results suggest that there is a metal-induced tradeoff between overall protein stability and metal coordination in members of the MCO family.