Phosphorylation and dephosphorylation modulation of an inverse temperature transition

Programmability and biomedical utility of intrinsically-disordered protein polymers

Intrinsically disordered proteins (IDPs) exhibit molecular-level conformational dynamics that are functionally harnessed across a wide range of fascinating biological phenomena. The low sequence complexity of IDPs has led to the design and development of intrinsically-disordered protein polymers (IDPPs), a class of engineered repeat IDPs with stimuli-responsive properties. The perfect repetitive architecture of IDPPs allows for repeat-level encoding of tunable protein functionality. Designer IDPPs can be modeled on endogenous IDPs or engineered de novo as protein polymers with dual biophysical and biological functionality. Their properties can be rationally tailored to access enigmatic IDP biology and to create programmable smart biomaterials. With the goal of inspiring the bioengineering of multifunctional IDP-based materials, here we synthesize recent multidisciplinary progress in programming and exploiting the bio-functionality of IDPPs and IDPP-containing proteins. Collectively, expanding beyond the traditional sequence space of extracellular IDPs, emergent sequence-level control of IDPP functionality is fueling the bioengineering of self-assembling biomaterials, advanced drug delivery systems, tissue scaffolds, and biomolecular condensates -genetically encoded organelle-like structures. Looking forward, we emphasize open challenges and emerging opportunities, arguing that the intracellular behaviors of IDPPs represent a rich space for biomedical discovery and innovation. Combined with the intense focus on IDP biology, the growing landscape of IDPPs and their biomedical applications set the stage for the accelerated engineering of high-value biotechnologies and biomaterials.

Temperature-Responsive Nano-Biomaterials from Genetically Encoded Farnesylated Disordered Proteins

Despite broad interest in understanding the biological implications of protein farnesylation in regulating different facets of cell biology, the use of this post-translational modification to develop protein-based materials and therapies remains underexplored. The progress has been slow due to the lack of accessible methodologies to generate farnesylated proteins with broad physicochemical diversities rapidly. This limitation, in turn, has hindered the empirical elucidation of farnesylated proteins' sequence-structure-function rules. To address this gap, we genetically engineered prokaryotes to develop operationally simple, high-yield biosynthetic routes to produce farnesylated proteins and revealed determinants of their emergent material properties (nano-aggregation and phase-behavior) using scattering, calorimetry, and microscopy. These outcomes foster the development of farnesylated proteins as recombinant therapeutics or biomaterials with molecularly programmable assembly.

Cracking the Skin Barrier: Liquid-Liquid Phase Separation Shines under the Skin

Central to forming and sustaining the skin’s barrier, epidermal keratinocytes (KCs) fluxing to the skin surface undergo a rapid and enigmatic transformation into flat, enucleated squames. At the crux of this transformation are intracellular keratohyalin granules (KGs) that suddenly disappear as terminally differentiating KCs transition to the cornified skin surface. Defects in KGs have long been linked to skin barrier disorders. Through the biophysical lens of liquid-liquid phase separation (LLPS), these enigmatic KGs recently emerged as liquid-like membraneless organelles whose assembly and subsequent pH-triggered disassembly drive squame formation. To stimulate future efforts toward cracking the complex process of skin barrier formation, in this review, we integrate the key concepts and foundational work spanning the fields of LLPS and epidermal biology. We review the current progress in the skin and discuss implications in the broader context of membraneless organelles across stratifying epithelia. The discovery of environmentally sensitive LLPS dynamics in the skin points to new avenues for dissecting the skin barrier and for addressing skin barrier disorders. We argue that skin and its appendages offer outstanding models to uncover LLPS-driven mechanisms in tissue biology.

High Throughput Screening of Dynamic Silk-Elastin-Like Protein Biomaterials

The need for dynamic, elastomeric polymeric biomaterials remains high, with few options with tunable control of mechanical properties, and environmental responses. Yet the diversity of these types of protein polymers pursued for biomaterials-related needs remains limited. Robust high-throughput synthesis and characterization methods will address the need to expand options for protein-polymers for a range of applications. To address this need, a combinatorial library approach with high throughput screening is used to select specific examples of dynamic protein silk-elastin-like polypeptides (SELPs) with unique stimuli responsive features, including tensile strength, and adhesion. Using this approach 64 different SELPs with different sequences and molecular weights are selected out of over 2,000 recombinant E. coli colonies. New understanding of sequence-function relationships with this family of proteins is gained through this combinatorial-screening approach and can provide a guide to future library designs. Further, this approach yields new families of SELPs to match specific material functions.

Triple stimulus-responsive polypeptide nanoparticles that enhance intratumoral spatial distribution

To address the limited tumor penetration of nanoparticle drug delivery vehicles, we report the first pH-responsive polypeptide micelle that dissociates at the low extracellular pH of solid tumors. This histidine-rich elastin-like polypeptide block copolymer self-assembles at 37 °C into spherical micelles that are stabilized by Zn(2+) and are disrupted as the pH drops from 7.4 to 6.4. These pH-sensitive micelles demonstrate better in vivo penetration and distribution in tumors than a pH-insensitive control.

Hierarchical and Modulable Hydrophobic Folding and Self-assembly in Elastic Protein-based Polymers: Implications for Signal Transduction

When the hydrophobic (apolar) and polar moieties of elastomeric polypeptides are properly balanced, the polypeptides are soluble in water at lower temperatures but undergo folding and assembly transitions to increased order on raising the temperature. The temperatures, Tt, and heats, ΔHt, of these inverse temperature transitions are determined by differential scanning calorimetry for a series of elastomeric polypentapeptides: poly(VPAVG), poly(IPAVG), poly(VPGVG), poly(IPGVG), poly[0.5(VPGVG),0.5(IPGVG)] and poly[0.82(IPGVG),0.18(IPGEG)] where V = Val, P = Pro, A = Ala, G = Gly, I = lle and E = Glu.

On increasing the hydrophobicity as when replacing V(Val) by I(lle) which is the addition of one CH2 moiety per pentamer, the temperature of the transition is lowered by 15 to 20°C and the heat of the transition is increased by more than one kcal/mole, for the above examples, by more than a factor of two.

When differential scanning calorimetry thermograms are obtained on mixtures of poly(VPAVG) plus poly(IPAVG) or of poly(VPGVG) plus poly(IPGVG), it is found that the polypentapeptides self-separate, i.e., they de-mix, even though in the latter case the conformations have been shown to be essentially identical before and after their respective transitions.

When the polymer, poly[0.82(IPGVG),0.18(IPGEG)], is studied as a function of pH, increasing the degree of ionization is found to increase the temperature and to decrease the heat of the transition such that, with the correct balance of I with the variable E(GluCOO−), the values of Tt and ΔHt can be made to approach those of poly(VPGVG). Acid-base titration studies indicate that less than one Glu(COO−) in 200 residues can raise the value of Tt by 25°C and decrease ΔHt by 90%.

These and additional data are interpreted to mean that there exists an hierarchical hydrophobic folding, that the hierarchical hydrophobic folding can be modulated by changing the degree of ionization or by changes in a number of intensive variables, that changes in these intensive variables can be used to drive folding/unfolding-assembly/disassembly transitions under isothermal conditions, and that these unfolding/folding and disassembly/assembly transitions can be used to achieve signal transduction. This is called the ΔTt mechanism of free energy (signal) transduction.

Properties And Prevention of Adhesions Applications of Bioelastic Materials

The origins, syntheses, variable composition and physical properties of bioelastic materials are discussed. The latter includes their capacity to undergo inverse temperature transitions to increased order on raising the temperature and to be designable to interconvert free energies involving the intensive variables of mechanical force, temperature, pressure, chemical potential, electrochemical potential and light.

Bioelastic materials include analogues and other chemical variations of the viscoelastic polypeptide, poly(Val-Pro-Gly-Val-Gly), and cross-linked elastomeric matrices thereof. This parent material has been shown to be remarkably biocompatible; it can be minimally modified to vary the rate of hydrolytic breakdown; it can contain enzymatically reactive sites; and it can have cell attachment sites included which promote excellent cell adhesion, spreading and growth to confluence.

One specific application is in the prevention of postoperative adhesion. There are some 30,000,000 per year surgical procedures in this country and a large portion of these would benefit if a suitable material were available for preventing adhesions. Bioelastic materials have been tested in a contaminated peritoneal model, and promising preliminary studies have been carried out in the rabbit eye model for strabismus surgery. In the peritoneal model, 90% of the 29 control animals exhibited significant adhesions; whereas, only 20% of the 29 animals using gas sterilized matrices had significant adhesions. On the basis of this data, it appears that cross-linked poly(VPGVG) is an effective physical barrier to adhesion formation in a trauma model with resulting hemorrhage and contamination.

The potential use of bioelastic materials as a pericardial substitute following the more than 400,000 open heart surgeries per year in the U.S. is under development beginning with the use of bioelastic matrices to prevent adhesions to the total artificial heart being used as a bridge to heart transplantation such that the site will be less compromised when receiving the donor heart.

Effect of phosphorylation on the thermal and light stability of the thylakoid membranes

Higher plant thylakoid membranes contain a protein kinase that phosphorylates certain threonine residues of light-harvesting complex II (LHCII), the main light-harvesting antenna complexes of photosystem II (PSII) and some other phosphoproteins (Allen, Biochim Biophys Acta 1098:275, 1992). While it has been established that phosphorylation induces a conformational change of LHCII and also brings about changes in the lateral organization of the thylakoid membrane, it is not clear how phosphorylation affects the dynamic architecture of the thylakoid membranes. In order to contribute to the elucidation of this complex question, we have investigated the effect of duroquinol-induced phosphorylation on the membrane ultrastructure and the thermal and light stability of the chiral macrodomains and of the trimeric organization of LHCII. As shown by small angle neutron scattering on thylakoid membranes, duroquinol treatment induced a moderate (~10%) increase in the repeat distance of stroma membranes, and phosphorylation caused an additional loss of the scattering intensity, which is probably associated with the partial unstacking of the granum membranes. Circular dichroism (CD) measurements also revealed only minor changes in the chiral macro-organization of the complexes and in the oligomerization state of LHCII. However, temperature dependences of characteristic CD bands showed that phosphorylation significantly decreased the thermal stability of the chiral macrodomains in phosphorylated compared to the non-phosphorylated samples (in leaves and isolated thylakoid membranes, from 48.3 degrees C to 42.6 degrees C and from 47.5 degrees C to 44.3 degrees C, respectively). As shown by non-denaturing PAGE of thylakoid membranes and CD spectroscopy on EDTA washed membranes, phosphorylation decreased by about 5 degrees C, the trimer-to-monomer transition temperature of LHCII. It also enhanced the light-induced disassembly of the chiral macrodomains and the monomerization of the LHCII trimers at 25 degrees C. These data strongly suggest that phosphorylation of the membranes considerably facilitates the heat- and light-inducible reorganizations in the thylakoid membranes and thus enhances the structural flexibility of the membrane architecture.

Effects of temperature and pressure on the aggregation properties of an engineered elastin model polypeptide in aqueous solution

The pressure and temperature dependence of the cloud point transition of an aqueous solution of an elastin-like polypeptide (MGLDGSMG(VPGIG)40VPLE), prepared by bacterial expression of the corresponding artificial gene, was measured. A temperature-pressure diagram was constructed over a wide range of conditions. The (VPGIG)40 solution exhibited a well-defined pressure-induced cloudpoint (Pc), as well as a temperature-induced transition (Tc). From near atmospheric pressure up to 100 MPa, Tc increased with increasing pressure, but decreased with further increases in pressure above 200 MPa. The maximum Tc was reached at 100-200 MPa. Between 10 and 25 degrees C, the Pc decreased with increasing temperature, and a broad maximum in Pc was observed in the range -10 to 0 degree C. These results are compared with our previous results on synthetic thermoresponsive vinyl polymers.

Phosphorylated tau can promote tubulin assembly

Phosphorylation can affect the function of microtubule-associated protein tau. Here, the human brain tau with 441 amino acids was phosphorylated by cyclic-AMP-dependent protein kinase (PKA) or glycogen synthase kinase-3beta. PKA-phosphorylated tau (2.7 mol phosphates/mol) does not promote tubulin assembly as judged by spectrophotometric and atomic force microscopy measurements, unless trimethylamine N-oxide (TMAO), a natural occurring osmolyte, is included in these assays. TMAO is also found to promote tubulin assembly of glycogen synthase kinase-3beta-phosphorylated tau (1.6 mol phosphates/mol). TMAO does not act by causing a chemical dephosphorylation of phosphorylated tau, but it acts to overcome the functional deficit caused by phosphorylation. PKA-phosphorylated tau binds to tubulin in the presence of TMAO and lowers the critical concentration of tubulin needed for assembly. From these data, we conclude that PKA-phosphorylated tau retains the ability to bind tubulin and promote tubulin assembly. TMAO is required, however, to sensitize the reaction. Possible uses of TMAO in relation to studies of tubulin assembly in vitro, in intact cells, and in relation to Alzheimer's disease are presented in this report.

Effect of citrulline for arginine replacement on the structure and turnover of phosphopeptide substrates of protein phosphatase-1

Phosphorylated and nonphosphorylated forms of a decapeptide corresponding to residues 9 to 18 of glycogen phosphorylase were compared using two-dimensional nuclear magnetic resonance with assignment of both peptides done by the sequential method. Both forms had little secondary structure, but there was evidence for an interaction between arginine-16 and phosphorylated serine at position 14. A change in the chemical shift for the epsilon-nitrogen hydrogen of arginine in position 16 was observed in the spectrum of the phosphorylated peptide and was not evident in a phosphopeptide having citrulline in place of arginine-16. Hydrolysis catalyzed by protein phosphatase-1 was decreased with the citrulline-containing phosphopeptide compared to the arginine-containing phosphopeptide with effects observed on both kcat and Km of the phosphatase reaction. Alkaline phosphatase hydrolyzed these peptides and a di-citrulline peptide equally well. These results are consistent with arginine being favorable in the recognition of substrates by phosphatase-1, possibly recognition as an arginine-phosphoserine complex. As a model study, arginine and two analogs, citrulline and canavanine, were examined for association with inorganic phosphate by nuclear magnetic resonance spectrometry. 31P-NMR measurements showed that arginine and canavanine caused a shift in the phosphate resonance at 20 degreesC. Citrulline caused no change. Changes in chemical shift were measured over the pH range 5-9 with arginine and canavanine both causing a slight decrease in the apparent pKa of inorganic phosphate (DeltapKa approximately 0.15). NaCl, NH4Cl, and guanidine hydrochloride showed little effect on the resonance signal position of inorganic phosphate at pH 6.5, consistent with selectivity for the guanidino group. Temperature (6 degrees, 20 degrees, and 37 degreesC) caused little change in the effect of arginine, but there was some dependency with canavanine, decreasing with temperature. Citrulline caused no change in the chemical shift of phosphate at any temperature. It was concluded that hydrogen bonded complexes were formed between the dianion of phosphate and the protonated form of arginine or canavanine with a bifurcated structure having preference for the omega-hydrogens.

Engineering protein-based machines to emulate key steps of metabolism (biological energy conversion)

Metabolism is the conversion of available energy sources to those energy forms required for sustaining and propagating living organisms; this is simply biological energy conversion. Proteins are the machines of metabolism; they are the engines of motility and the other machines that interconvert energy forms not involving motion. Accordingly, metabolic engineering becomes the use of natural protein-based machines for the good of society. In addition, metabolic engineering can utilize the principles, whereby proteins function, to design new protein-based machines to fulfill roles for society that proteins have never been called upon throughout evolution to fulfill. This article presents arguments for a universal mechanism whereby proteins perform their diverse energy conversions; it begins with background information, and then asserts a set of five axioms for protein folding, assembly, and function and for protein engineering. The key process is the hydrophobic folding and assembly transition exhibited by properly balanced amphiphilic protein sequences. The fundamental molecular process is the competition for hydration between hydrophobic and polar, e.g., charged, residues. This competition determines Tt, the onset temperature for the hydrophobic folding and assembly transition, Nhh, the numbers of waters of hydrophobic hydration, and the pKa of ionizable functions. Reported acid-base titrations and pH dependence of microwave dielectric relaxation data simultaneously demonstrate the interdependence of Tt, Nhh and the pKa using a series of microbially prepared protein-based poly(30mers) with one glutamic acid residue per 30mer and with an increasing number of more hydrophobic phenylalanine residues replacing valine residues. Also, reduction of nicotinamides and flavins is shown to lower Tt, i.e., to increase hydrophobicity. Furthermore, the argument is presented, and related to an extended Henderson-Hasselbalch equation, wherein reduction of nicotinamides represents an increase in hydrophobicity and resulting hydrophobic-induced pKa shifts become the basis for understanding a primary energy conversion (proton transport) process of mitochondria. Copyright 1998 John Wiley & Sons, Inc.

Elastic protein-based materials in tissue reconstruction

In natural tissues, cells form multiple attachment sites to their extracellular matrix. By means of those attachments, cells deform as the tissue deforms in response to the natural mechanical stresses and strains that the tissue must sustain during function. These mechanical forces are the energy input that instruct the cells to produce the extracellular matrix sufficient to sustain those forces. Thus, an ideal artificial material should have both the attachment sites for the natural cells and a compliance that matches the natural tissue. Elastic protein-based polymers have been designed to provide both cell attachment sites and to exhibit the required elastic modulus of the tissue to be replaced. Thus, this introduces the potential to design a temporary functional scaffolding that will be remodeled, while functioning, into a natural tissue. A feasibility study applies this concept to the problem of urinary bladder reconstruction in terms of the filling and emptying of a simulated bladder comprised of an elastic protein-based matrix containing cell attachment sites with human urothelial cells growing out onto the dynamic matrix. Furthermore, the elastic protein-based materials themselves have been designed to perform the set of energy conversions that occur in living organisms and, in particular, to convert mechanical energy into chemical energy with the result of chemical signals of the sort that could provide the stimuli to turn on the genes for producing the required extracellular proteins.

A photogenerated pore-forming protein

BACKGROUND

The permeabilization of cells with bacterial pore-forming proteins is an important technique in cell biology that allows the exchange of small reagents into the cytoplasm of a cell. Another notable technology is the use of caged molecules whose activities are blocked by addition of photoremovable protecting groups. This allows the photogeneration of reagents on or in cells with spatial and temporal control. Here, we combine these approaches to produce a caged pore-forming protein for the controlled permeabilization of cells.

RESULTS

2-Bromo-2-(2-nitrophenyl)acetic acid (BNPA), a water-soluble cysteine-directed reagent for caging peptides and proteins with the alpha-carboxy-2-nitrobenzyl (CNB) protecting group, was synthesized. Glutathione (gamma-Glu-Cys-Gly) was released in high yield from gamma-Glu-CysCNB-Gly by irradiation at 300 nm. Based on this finding, scanning mutagenesis was used to find a single-cysteine mutant of the pore-forming protein staphylococcal alpha-hemolysin (alpha HL) suitable for caging. When alpha HL-R104C was derivatized with BNPA, pore-forming activity toward rabbit erythrocytes was lost. Near UV irradiation led to regeneration of the cysteine sulfhydryl group and the restoration of pore-forming activity.

CONCLUSIONS

Caged pore-forming proteins are potentially useful for permeabilizing one cell in a collection of cells or one region of the plasma membrane of a single cell. Therefore, alpha HL-R104C-CNB and other caged proteins designed to create pores of various diameters should be useful for many purposes. For example, the ability to introduce reagents into one cell of a network or into one region of a single cell could be used in studies of neuronal modulation. Further, BNPA should be generally useful for caging cysteine-containing peptides and single-cysteine mutant proteins to study, for example, cell signaling or structural changes in proteins.

Triggers and switches in a self-assembling pore-forming protein

Protein engineering is being used to produce a collection of pore-forming proteins with applications in biotechnology. Knowledge provided by investigations of the mechanism of self-assembly of staphylococcal alpha-hemolysin has allowed the design of genetically and chemically modified variants of the protein with pore-forming activities that can be triggered or switched on-and-off by chemical, biochemical and physical inputs. Examples include alpha-hemolysins that are activated by specific proteases and alpha a-hemolysins whose activity is controlled by divalent metal ions. These proteins have potential value in drug delivery as components of immunotoxins that can be activated at the surfaces of target cells. Further applications are likely in improved encapsulation techniques for drugs, enzymes and cells.

Reduction-driven polypeptide folding by the delta Tt mechanism

Poly(Gly-Val-Gly-Val-Pro), i.e., poly(GVGVP), exhibits composition and solute dependence of Tt, the temperature of the inverse temperature transition at which hydrophobic folding and assembly occur on raising the temperature. Importantly, a means whereby the value of Tt is lowered from above to below the working temperature becomes an isothermal means of driving folding and assembly, i.e., of achieving free energy transduction. Using poly[0.73(GVGVP),0.27(GK[NMeN]GVP)] where [NMeN] indicates N-methyl nicotinamide attached to the epsilon-NH2 of the Lys(K) residue, chemical and electrochemical reductions are found to remarkably lower the value of Tt; reduction can drive hydrophobic folding and assembly as effectively as decreasing ionization. Changing the redox state of a protein becomes yet another means of achieving free energy transduction by the delta Tt mechanism.

Hydrophobicity scale for proteins based on inverse temperature transitions

In general, proteins fold with hydrophobic residues buried, away from water. Reversible protein folding due to hydrophobic interactions results from inverse temperature transitions where folding occurs on raising the temperature. Because homoiothermic animals constitute an infinite heat reservoir, it is the transition temperature, Tt, not the endothermic heat of the transition, that determines the hydrophobically folded state of polypeptides at body temperature. Reported here is a new hydrophobicity scale based on the values of Tt for each amino acid residue as a guest in a natural repeating peptide sequence, the high polymers of which exhibit reversible inverse temperature transitions. Significantly, a number of ways have been demonstrated for changing Tt such that reversibly lowering Tt from above to below physiological temperature becomes a means of isothermally and reversibly driving hydrophobic folding. Accordingly, controlling Tt becomes a mechanism whereby proteins can be induced to carry out isothermal free energy transduction.

Hydrophobicity-induced pK shifts in elastin protein-based polymers

Three polypentapeptides--poly[0.8(GVGVP), 0.2(GEGVP)], poly[0.8(GVGIP), 0.2(GEGIP)], and poly[0.75(GFGVP), 0.25(GEGVP)]--all analogues of the polypentapeptide of elastin--(Val1-Pro2-Gly3-Val4-Gly5)n or poly(VPGVG)--have been prepared to determine the effect of changing the hydrophobicity, i.e., Val1----Ile1 (I) and Val4----Phe4 (F), on the pKa and the temperature dependence of pKa of the Glu (E) residue. Shifts in pKa as large as 1.7 units are observed and the temperature dependence is much steeper for the structure-dependent proximity of the more hydrophobic Ile1 residues to the Glu4 residue. Even though this system is dominated by the inverse temperature transition of hydrophobically driven folding on raising the temperature, the effect of adding 0.15 N NaCl is to suppress the hydrophobicity-induced pKa shift.