Design of protein conformational switches

Protein conformational switches are ubiquitous in nature and often regulate key biological processes. To design new proteins that can switch conformation, protein designers have focused on the two key components of protein switches: the amino acid sequence must be compatible with the multiple target states and there must be a mechanism for perturbing the relative stability of these states. Proteins have been designed that can switch between folded and disordered states, between distinct folded states and between different aggregation states. A variety of trigger mechanisms have been used, including pH shifts, post-translational modification and ligand binding. Recently, computational protein design methods have been applied to switch design. These include algorithms for designing novel ligand-binding sites and simultaneously optimizing a sequence for multiple target structures.     

Time-delayed model of RNA interference

RNA interference (RNAi) is a fundamental cellular process that inhibits gene expression through cleavage and destruction of target mRNA. It is responsible for a number of important intracellular functions, from being the first line of immune defence against pathogens to regulating development and morphogenesis. In this paper we consider a mathematical model of RNAi with particular emphasis on time delays associated with two aspects of primed amplification: binding of siRNA to aberrant RNA, and binding of siRNA to mRNA, both of which result in the expanded production of dsRNA responsible for RNA silencing. Analytical and numerical stability analyses are performed to identify regions of stability of different steady states and to determine conditions on parameters that lead to instability. Our results suggest that while the original model without time delays exhibits a bi-stability due to the presence of a hysteresis loop, under the influence of time delays, one of the two steady states with the high (default) or small (silenced) concentration of mRNA can actually lose its stability via a Hopf bifurcation. This leads to the co-existence of a stable steady state and a stable periodic orbit, which has a profound effect on the dynamics of the system.     

Free-energy simulations of the oxidation of c-terminal methionines in calmodulin

In the course of aging or under conditions of oxidative stress, methionine residues of calmodulin undergo oxidation, leading to loss of biological activity of the protein. We have performed free-energy simulations of the effects of C-terminal methionine side-chain oxidation on the properties of calmodulin. The simulation results indicate that oxidation should have a destabilizing effect on all three protein functional states: calcium free, calcium loaded, and with both calcium and target peptide bound. Because the different states are destabilized by different amounts, this leads to a more complex pattern in the observable effects on protein thermal stability, calcium affinity, and binding of a target peptide. The influence of oxidation on the free energy of CaM unfolding is estimated by comparing the free-energy cost of oxidizing a Met residue in a Gly-Met-Gly peptide and in the protein. The protein thermal stability of the oxidized forms is lowered by a moderate amount 1-3 kcal/mol, in qualitative agreement with experimental results of 0.3 kcal/mol. The calculated changes in affinity for calcium and for the target peptide show opposing trends. Oxidation at position 144 is predicted to enhance peptide binding and weaken calcium binding, whereas oxidation at 145 weakens peptide binding and enhances affinity for calcium. The lower affinity of Met 145-oxidized calmodulin toward the target peptide correlates with experimentally observed lowering of calmodulin-activated Ca-ATPase activity when oxidized calmodulin from aged rat brains is used. Thus, our simulations suggest that Met 145 is the oxidation site in the C-terminal fragment of calmodulin. The microscopic mechanism behind the calculated free energy changes appears to be a greater affinity for water of the oxidized Met side-chain relative to normal Met. Structures with Met exposed to solvent had consistently lower free energies than those with buried Met sidechains.     

Evolutionary models and the normative significance of stability

Many have expected that understanding the evolution of norms should, in some way, bear on our first-order normative outlook: How norms evolve should shape which norms we accept. But recent philosophy has not done much to shore up this expectation. Most existing discussions of evolution and norms either jump headlong into the is/ought gap or else target meta-ethical issues, such as the objectivity of norms. My aim in this paper is to sketch a different way in which evolutionary considerations can feed into normative thinking—focusing on stability. I will discuss two (related) forms of argument that utilize information about social stability drawn from evolutionary models, and employs it to assess claims in political philosophy. One such argument treats stability as feature of social states that may be taken into account alongside other features. The other uses stability as a constraint on the realization of social ideals, via a version of the ought-implies-can maxim. These forms of argument are not new; indeed they have a history going back at least to early modern philosophy. But their marriage with evolutionary information is relatively recent, has a significantly novel character, and has received little attention in recent moral and political philosophy.     

Solution stability of salmon calcitonin at high concentration for delivery in an implantable system.

Salmon calcitonin solutions (50 mg/mL and 100 mg/mL) were placed on stability at 37 degrees C for 1 year in a variety of solvent systems including water, ethanol, glycerol, propylene glycol (PG) and dimethyl sulfoxide (DMSO). Calcitonin degradation was monitored by RP-HPLC and size-exclusion chromatography. DMSO and pH 3.3 solutions provided optimum stability. Conformational stability was also monitored by FTIR over the 1 year time course and compared with chemical and physical stability. After 12 months at 37 degrees C, four major conformations were observed: a beta-sheet conformation (pH 3.3, pH 5.0, 70% DMSO and 70% glycerol), an aggregate conformation (pH 7.0 water), a strong alpha-helical conformation (70% EtOH, 70% PG) and a weak alpha-helical conformation (100% DMSO). No correlation between structure and chemical stability was observed in which both the beta-sheet structure (pH 3.3, water) and a loose alpha-helical structure (100% DMSO) demonstrated good stability. However, some correlation was observed between structure and physical stability, where co-solvents inducing an alpha-helical structure resulted in a decrease in gelation. These two structural states associated with improved stability and minimal gelation, indicated that gelation can be reduced or eliminated by the use of pharmaceutically acceptable co-solvents. Finally, salmon calcitonin (50 mg/mL) was formulated in 100% DMSO and delivered from a DUROS implant over 4 months. Delivery at a target dose of 18 microg/day calcitonin at 37 degrees C was confirmed.     

Threshold extraction in metabolite concentration data

MOTIVATION: Continued development of analytical techniques based on gas chromatography and mass spectrometry now facilitates the generation of larger sets of metabolite concentration data. An important step towards the understanding of metabolite dynamics is the recognition of stable states where metabolite concentrations exhibit a simple behaviour. Such states can be characterized through the identification of significant thresholds in the concentrations. But general techniques for finding discretization thresholds in continuous data prove to be practically insufficient for detecting states due to the weak conditional dependences in concentration data. RESULTS: We introduce a method of recognizing states in the framework of decision tree induction. It is based upon a global analysis of decision forests where stability and quality are evaluated. It leads to the detection of thresholds that are both comprehensible and robust. Applied to metabolite concentration data, this method has led to the discovery of hidden states in the corresponding variables. Some of these reflect known properties of the biological experiments, and others point to putative new states. AVAILABILITY: An implementation of this approach can be obtained from the authors upon request.     

Native protein sequences are designed to destabilize folding intermediates

Hydrophobic core mutants of sperm whale apomyoglobin were constructed to investigate the amino acid sequence features that determine the folding properties. Replacements of all of the Ile residues with Leu and of all of the Ile and Val residues with Leu decreased the thermodynamic stability of the folded states against the unfolded states but increased the stability of the folding intermediates against the unfolded states, indicating that the amino acid composition of the protein core is important for the protein stability and folding cooperativity. To examine the effect of the arrangement of these hydrophobic residues, mutant proteins were further constructed: 12 sites out of the 18 Leu, 9 Ile, and 8 Val residues of the wild-type myoglobin were randomly replaced with each other so that the amino acid compositions were similar to that of the wild-type protein. Four mutant proteins were obtained without selection of the protein properties. These residue replacements similarly resulted in the stabilization of both the intermediate and folded states against the unfolded states, as compared to the wild-type protein. Thus, the arrangements of the hydrophobic residues in the native amino acid sequence are selected to destabilize the folding intermediate rather than to stabilize the folded state. The present results suggest that the two-state transition of protein folding or the transient formation of the unstable intermediate, which seems to be required for effective production of the functional proteins, has been a major driving force in the molecular evolution of natural globular proteins.     

Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study

Environmental variables can exert significant influences on the folding stability of a protein, and elucidating these influences provides insight on the determinants of protein stability. Here, experimental data on the stability of FKBP12 are reported for the effects of three environmental variables: pH, salt, and macromolecular crowding. In the pH range of 5-9, contribution to the pH dependence of the unfolding free energy from residual charge-charge interactions in the unfolded state was found to be negligible. The negligible contribution was attributed to the lack of sequentially nearest neighboring charged residues around groups that titrate in the pH range. KCl lowered the stability of FKBP12 and the E31Q/D32N double mutant at small salt concentrations but raised stability after approximately 0.5 M salt. Such a turnover behavior was accounted for by the balance of two opposing types of protein-salt interactions: the Debye-Hückel type, modeling the response of the ions to protein charges, favors the unfolded state while the Kirkwood type, accounting for the disadvantage of the ions moving toward the low-dielectric protein cavity from the bulk solvent, disfavors the unfolded state. Ficoll 70 as a crowding agent was found to have a modest effect on protein stability, in qualitative agreement with a simple model suggesting that the folded and unfolded states are nearly equally adversely affected by macromolecular crowding. For any environmental variable, it is the balance of its effects on the folded and unfolded states that determines the outcome on the folding stability.     

Impossibility of multiple steady states in a family of active membrane transport models

To study the dynamical behavior of active membrane transport models, Vieira and Bisch proposed a complex chemical network (model 3) with two cycles. One cycle involves monomers as pump units while the other cycle uses dimers. In their work, the stoichiometric network analysis was used to study the stability of steady states and the bifurcation analysis was done through numerical methods. They concluded that the possibility of multiple steady states in the model 3 could not be discarded. Here, a zero eigenvalue analysis is applied to prove the impossibility of multiple positive steady states in the model 3. (A positive steady state is one for which all species have positive concentrations.) Moreover, the result is generalized to its family networks. Received: 6 April 1998 / Revised version: 16 October 1998 / Accepted: 28 October 1998     

Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies

A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy minimized structures lack understanding of the dynamic DNA–ion interaction. The present work addresses these questions by molecular dynamics simulation studies on two DNA duplexes and their interaction with magnesium ions. Results show typical B-DNA character with occasional excursions to deviated states. We detected expected stability of the duplexes in terms of backbone conformations and base pair parameter by the CHARMM-27 force field. Ion environment analysis shows that Mg²⁺ retains the coordination sphere throughout the simulation with a preference for major groove over minor. An extensive analysis of the influence of the Mg²⁺ ion shows no evidence of the popular predictions of groove width narrowing by dipositive metal ion. The major groove atoms show higher occupancy and residence time compared to minor groove for magnesium, where no such distinction is found for the charge neutralizing Na⁺ ions. The determining factor of Mg²⁺ ion’s choice in DNA binding site evolves as the steric hindrance faced by the bulky hexahydrated cation where wider major groove gets the preference. We have shown that in case of binding of Mg²⁺ to DNA non electrostatic contributions play a major role.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:5     

Boolean network-based analysis of the apoptosis network: Irreversible apoptosis and stable surviving

To understand the design principles of the molecular interaction network associated with the irreversibility of cell apoptosis and the stability of cell surviving, we constructed a Boolean network integrating both the intrinsic and extrinsic pro-apoptotic pathways with pro-survival signal transduction pathways. We performed statistical analyses of the dependences of cell fate on initial states and on input signals. The analyses reproduced the well-known pro- and anti-apoptotic effects of key external signals and network components. We found that the external GF signal by itself did not change the apoptotic ratio from randomly chosen initial states when there is no external TNF signal, but can significantly offset apoptosis induced by the TNF signal. While a complete model produces the expected irreversibility of the apoptosis process, alternative models missing one or more of four selected inter-component connections indicate that the feedback loops directly involving the caspase 3 are essential for maintaining irreversibility of apoptosis. The feedback loops involving P53 showed compensating effects when those involving caspase 3 have been removed. The GF signal significantly increases the stability of the surviving states of the network. The apoptosis network seems to use different modules by design to control the irreversibility of the apoptosis process and the stability of the surviving states. Such a design may accommodate the needed plasticity for the network to adapt to different cellular environments: depending on the strength of external pro-surviving signals, apoptosis can be induced either easily or difficultly by pro-apoptotic signal of varying strengths, but proceed with invariable irreversibility.     

Engineering the robustness of industrial microbes through synthetic biology

Microbial fermentations and bioconversions play a central role in the production of pharmaceuticals, enzymes and chemicals. To meet the demands of industrial production, it is desirable that microbes maintain a maximized carbon flux towards target metabolites regardless of fluctuations in intracellular or extracellular environments. This requires cellular systems that maintain functional stability and dynamic homeostasis in a given physiological state, or manipulate transitions between different physiological states. Stable maintenance or smooth transition can be achieved through engineering of dynamic controllability, modular and hierarchical organization, or functional redundancy, three key features of biological robustness in a cellular system. This review summarizes how synthetic biology can be used to improve the robustness of industrial microbes.     

Modeling the adaptive immune response in HBV infection

The aim of this work is to investigate a new mathematical model that describes the interactions between Hepatitis B virus (HBV), liver cells (hepatocytes), and the adaptive immune response. The qualitative analysis of this as cytotoxic T lymphocytes (CTL) cells and the antibodies. These outcomes are (1) a disease free steady state, which its local stability is characterized as usual by R ₀ < 1, (2) and the existence of four endemic steady states when R ₀ > 1. The local stability of these steady states depends on functions of R ₀. Our study shows that although we give conditions of stability of these steady states, not all conditions are feasible. This rules out the local stability of two steady states. The conditions of stability of the two other steady states (which represent the complete failure of the adaptive immunity and the persistence of the disease) are formulated based on the domination of CTL cells response or the antibody response.     

Memory in idiotypic networks due to competition between proliferation and differentiation

A model employing separate dose-dependent response functions for proliferation and differentiation of idiotypically interacting B cell clones is presented. For each clone the population dynamics of proliferating B cells, non-proliferating B cells and free antibodies are considered. An effective response function, which contains the total impact of proliferation and differentiation at the fixed points, is defined in order to enable an exact analysis. The analysis of the memory states is restricted in this paper to a two-species system. The conditions for the existence of locally stable steady states with expanded B cell and antibody populations are established for various combinations of different field-response functions (e.g. linear, saturation, log-bell functions). The stable fixed points are interpreted as memory states in terms of immunity and tolerance. It is proven that a combination of linear response functions for both proliferation and differentiation does not give rise to stable fixed points. However, due to competition between proliferation and differentiation saturation response functions are sufficient to obtain two memory states, provided proliferation preceeds differentiation and also saturates earlier. The use of log-bell-shaped response functions for both proliferation and differentiation gives rise to a “mexican-hat” effective response function and allows for multiple (four to six) memory states. Both a primary response and a much more pronounced secondary response are observed. The stability of the memory states is studied as a function of the parameters of the model. The attractors lose their stability when the mean residence time of antibodies in the system is much longer than the B cells' lifetime. Neither the stability results nor the dynamics are qualitatively chanbed by the existence of non-proliferating B cells: memory states can exist and be stable without non-proliferating B cells. Nevertheless, the activation of non-proliferating B cells and the competition between proliferation and differentiation enlarge the parameter regime for which stable attractors are found. In addition, it is shown that a separate activation step from virgin to active B cells renders the virgin state stable for any choice of biologically reasonable parameters.     

Towards a tunable molecular memory that fits into a (10 Å)3 cube

Using DFT calculations we predict a novel family of small amino acid-based memory-exhibiting molecules, namely complexes of triply deprotonated cysteine (or its derivatives) with selected hexavalent transition metals. We show that the energy difference of the 0 and 1 electromers--corresponding to two chemically distinct oxidation states of a metal, M(VI) and M(IV)--can be tuned towards the thermodynamic equilibrium via deliberate chemical substitutions in the cysteine ligand. Although the thermal stability of both electromers is computed to be rather small at ambient temperatures (due to facile interchange of states 0 and 1 via a low-lying M(V) configuration), we hope to improve stability in related systems. [Figure: see text]. We propose novel kind of tunable molecular memory, based on intramolecular 2e- redox reaction.     

Two-step recruitment of RNA-directed DNA methylation to tandem repeats

Tandem repeat sequences are frequently associated with gene silencing phenomena. The Arabidopsis thaliana FWA gene contains two tandem repeats and is an efficient target for RNA-directed de novo DNA methylation when it is transformed into plants. We showed that the FWA tandem repeats are necessary and sufficient for de novo DNA methylation and that repeated character rather than intrinsic sequence is likely important. Endogenous FWA can adopt either of two stable epigenetic states: methylated and silenced or unmethylated and active. Surprisingly, we found small interfering RNAs (siRNAs) associated with FWA in both states. Despite this, only the methylated form of endogenous FWA could recruit further RNA-directed DNA methylation or cause efficient de novo methylation of transgenic FWA. This suggests that RNA-directed DNA methylation occurs in two steps: first, the initial recruitment of the siRNA-producing machinery, and second, siRNA-directed DNA methylation either in cis or in trans. The efficiency of this second step varies depending on the nature of the siRNA-producing locus, and at some loci, it may require pre-existing chromatin modifications such as DNA methylation itself. Enhancement of RNA-directed DNA methylation by pre-existing DNA methylation could create a self-reinforcing system to enhance the stability of silencing. Tandem repeats throughout the Arabidopsis genome produce siRNAs, suggesting that repeat acquisition may be a general mechanism for the evolution of gene silencing.