Amphiphilic 4-helix bundles designed for biomolecular materials applications

Protein Design: From the Aspect of Water Solubility and Stability

Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.

Designed di-heme binding helical transmembrane protein

De novo designing of functional membrane proteins is fundamental in terms of understanding the structure, folding, and stability of membrane proteins. In this work, we report the design and characterization of a transmembrane protein, termed HETPRO (HEme-binding Transmembrane PROtein), that binds two molecules of heme in a membrane and catalyzes oxidation/reduction reactions. The primary structure of HETPRO has been optimized in a guided fashion, from an antimicrobial peptide, for transmembrane orientation, defined 3D structure, and functions. HETPRO assembles into a tetrameric form, from an apo dimeric helical structure, in complex with cofactor in detergent micelles. The NMR structure of the apo HETPRO in micelles reveals an antiparallel helical dimer that inserts into the nonpolar core of detergent micelles. The well-defined structure of HETPRO and its ability to bind to heme moieties could be utilized to develop a functional membrane protein mimic for electron transport and photosystems.

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.

Control of the orientational order and nonlinear optical response of the "push-pull" chromophore RuPZn via specific incorporation into densely packed monolayer ensembles of an amphiphilic four-helix bundle peptide: characterization of the peptide-chromophore complexes

"Push-pull" chromophores based on extended pi-electron systems have been designed to exhibit exceptionally large molecular hyperpolarizabilities. We have engineered an amphiphilic four-helix bundle peptide to vectorially incorporate such hyperpolarizable chromophores having a metalloporphyrin moiety, with high specificity into the interior core of the bundle. The amphiphilic exterior of the bundle facilitates the formation of densely packed monolayer ensembles of the vectorially oriented peptide-chromophore complexes at the liquid-gas interface. Chemical specificity designed into the ends of the bundle facilitates the subsequent covalent attachment of these monolayer ensembles onto the surface of an inorganic substrate. In this article, we describe the structural characterization of these monolayer ensembles at each stage of their fabrication for one such peptide-chromophore complex designated as AP0-RuPZn. In the accompanying article, we describe the characterization of their macroscopic nonlinear optical properties.

Interferometric enhancement of x-ray reflectivity from unperturbed Langmuir monolayers of amphiphiles at the liquid-gas interface

Langmuir monolayers provide an important system for the investigation of the intramolecular structure and intermolecular ordering of organic and bio-organic macromolecular amphiphiles at an interface between polar and nonpolar media, e.g., the liquid-gas interface. Specular x-ray and neutron reflectivity have contributed substantially to these investigations. However, these reflectivity techniques are generally limited by the absence of crucial phase information, the relatively small contribution of the amphiphile to the scattering-length density contrast across the interface, and the relatively limited range of momentum transfer available perpendicular to the interface. Although several procedures have been developed to provide model-independent solutions to the phase problem, there remains a limited ability to distinguish features of slightly differing contrast (i.e., the "sensitivity") as well as their minimum allowable separation (i.e., the "spatial resolution") along the length of the scattering-length density profile derived from the reflectivity data via solution to the phase problem. Here, we demonstrate how the well-known interferometric approach can be extended to the structural investigation of otherwise unperturbed Langmuir monolayers of these amphiphiles to provide a direct solution to the phase problem and importantly, substantially enhance both the sensitivity and the spatial resolution in the derived profiles.

Portable UV-visible spectrometer for measuring absorbance and dichroism of Langmuir monolayers at air-water interfaces

An UV-visible spectrometer for measuring absorbance and dichroism of Langmuir monolayers under in situ conditions is described. The spectrometer utilizes a stand-alone multipass sensor, which is placed in a Langmuir trough and coupled with light source and spectrometer head via fiber optics. Implementation of the multipass scheme in the absorbance sensor makes it possible to obtain reliable quantitative spectroscopic data of the Langmuir monolayers with absorbance as low as 1 mOD. Such high sensitivity makes the developed sensor very useful for UV-visible spectral studies of a wide variety of chromophores. The new technique was applied to several model systems: fatty acid monolayers containing amphiphilic dyes DiI or BODIPY and also a monolayer of a synthetic amphiphilic porphyrin-binding peptide BBC16. Implementation of UV-visible absorbance spectroscopy measurements in situ together with x-ray scattering technique was used to confirm the bound state of the chromophore, and determine the exact position of the latter in the peptide matrix. Fiber optics design of the spectrometer provides portability and compatibility with other experimental techniques making it possible to study samples with a geometry unsuitable for conventional spectroscopic measurements and located in experimental environments with spatial limitations, such as synchrotron x-ray scattering stations.

New design of helix bundle peptide-polymer conjugates

We present a new design of peptide-polymer conjugates where a polymer chain is covalently linked to the side chain of a helix bundle-forming peptide. The effect of conjugated polymer chains on the peptide structure was examined using a de novo designed three-helix bundle and a photoactive four-helix bundle. Upon attachment of poly(ethylene glycol) to the exterior of the coiled-coil helix bundle, the peptide secondary structure was stabilized and the tertiary structure, that is, the coiled-coil helix bundle, was retained. When a heme-binding peptide as an example is used, the new peptide-polymer conjugate architecture also preserves the built-in functionalities within the interior of the helix bundle. It is expected that the conjugated polymer chains act to mediate the interactions between the helix bundle and its external environment. Thus, this new peptide-polymer conjugate design strategy may open new avenues to macroscopically assemble the helix bundles and may enable them to function in nonbiological environments.

Structure and dynamics of an extended conjugated NLO chromophore within an amphiphilic 4-helix bundle peptide by molecular dynamics simulation

Incorporation of extended conjugated chromophores into amphiphilic 4-helix bundle peptides has been shown experimentally to be an effective means to orient the chromphores vectorially in 2-D ensembles with high in-plane density. The designed microscopic hyperpolarizabilty of the chromophore is preserved in the macroscopic NLO response of the ensemble. We show via molecular dynamics simulation that the designed coiled-coil structure of the bundle controls the conformation and dynamics of the chromophore that are critical to optimizing its hyperpolarizability.

Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations

The three-dimensional structure and dynamics of de novo designed, amphiphilic four-helix bundle peptides (or "maquettes"), capable of binding metallo-porphyrin cofactors at selected locations along the length of the core of the bundle, are investigated via molecular dynamics simulations. The rapid evolution of the initial design to stable three-dimensional structures in the absence (apo-form) and presence (holo-form) of bound cofactors is described for the maquettes at two different soft interfaces between polar and nonpolar media. This comparison of the apo- versus holo-forms allows the investigation of the effects of cofactor incorporation on the structure of the four-helix bundle. The simulation results are in qualitative agreement with available experimental data describing the structures at lower resolution and limited dimension.

Incorporation of designed extended chromophores into amphiphilic 4-helix bundle peptides for nonlinear optical biomolecular materials

Multipigment ensembles that feature (porphinato)metal components and appropriate ethyne- and oligoyne-based chromophore-to-chromophore connectivity can manifest large optical polarizabilities and hyperpolarizabilities by design. Their vectorial orientation and local environment are controlled upon incorporation into designed amphiphilic 4-helix bundle peptides via axial histidyl ligation without disturbing the peptide's helical secondary structure. The chromophore/peptide stoichiometry can be tuned by varying the peptide's oligomeric state. The chromophore/peptide complexes are thermally stable, making them ideal candidates for the fabrication of nonlinear optical biomolecular materials.

Structural studies of amphiphilic 4-helix bundle peptides incorporating designed extended chromophores for nonlinear optical biomolecular materials

Extended conjugated chromophores containing (porphinato)zinc components that exhibit large optical polarizabilities and hyperpolarizabiliites are incorporated into amphiphilic 4-helix bundle peptides via specific axial histidyl ligation of the metal. The bundle's designed amphiphilicity enables vectorial orientation of the chromophore/peptide complex in macroscopic monolayer ensembles. The 4-helix bundle structure is maintained upon incorporation of two different chromophores at stoichiometries of 1-2 per bundle. The axial ligation site appears to effectively control the position of the chromophore along the length of the bundle.

Biomimetic membranes designed from amphiphilic block copolymers

A review dedicated to block copolymer self assembly. We discuss general progress in physicochemical interpretations and provide insight to recent developments in (hybrid) materials.

Monolayers of a model anesthetic-binding membrane protein: formation, characterization, and halothane-binding affinity

hbAP0 is a model membrane protein designed to possess an anesthetic-binding cavity in its hydrophilic domain and a cation channel in its hydrophobic domain. Grazing incidence x-ray diffraction shows that hbAP0 forms four-helix bundles that are vectorially oriented within Langmuir monolayers at the air-water interface. Single monolayers of hbAP0 on alkylated solid substrates would provide an optimal system for detailed structural and dynamical studies of anesthetic-peptide interaction via x-ray and neutron scattering and polarized spectroscopic techniques. Langmuir-Blodgett and Langmuir-Schaeffer deposition and self-assembly techniques were used to form single monolayer films of the vectorially oriented peptide hbAP0 via both chemisorption and physisorption onto suitably alkylated solid substrates. The films were characterized by ultraviolet absorption, ellipsometry, circular dichroism, and polarized Fourier transform infrared spectroscopy. The alpha-helical secondary structure of the peptide was retained in the films. Under certain conditions, the average orientation of the helical axis was inclined relative to the plane of the substrate, approaching perpendicular in some cases. The halothane-binding affinity of the vectorially oriented hbAP0 peptide in the single monolayers, with the volatile anesthetic introduced into the moist vapor environment of the monolayer, was found to be similar to that for the detergent-solubilized peptide.

Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales

Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.

Design of amphiphilic protein maquettes: controlling assembly, membrane insertion, and cofactor interactions

We have designed polypeptides combining selected lipophilic (LP) and hydrophilic (HP) sequences that assemble into amphiphilic (AP) alpha-helical bundles to reproduce key structure characteristics and functional elements of natural membrane proteins. The principal AP maquette (AP1) developed here joins 14 residues of a heme binding sequence from a structured diheme-four-alpha-helical bundle (HP1), with 24 residues of a membrane-spanning LP domain from the natural four-alpha-helical M2 channel of the influenza virus, through a flexible linking sequence (GGNG) to make a 42 amino acid peptide. The individual AP1 helices (without connecting loops) assemble in detergent into four-alpha-helical bundles as observed by analytical ultracentrifugation. The helices are oriented parallel as indicated by interactions typical of adjacent hemes. AP1 orients vectorially at nonpolar-polar interfaces and readily incorporates into phospholipid vesicles with >97% efficiency, although most probably without vectorial bias. Mono- and diheme-AP1 in membranes enhance functional elements well established in related HP analogues. These include strong redox charge coupling of heme with interior glutamates and internal electric field effects eliciting a remarkable 160 mV splitting of the redox potentials of adjacent hemes that leads to differential heme binding affinities. The AP maquette variants, AP2 and AP3, removed heme-ligating histidines from the HP domain and included heme-ligating histidines in LP domains by selecting the b(H) heme binding sequence from the membrane-spanning d-helix of respiratory cytochrome bc(1). These represent the first examples of AP maquettes with heme and bacteriochlorophyll binding sites located within the LP domains.

Design of amphiphilic protein maquettes: enhancing maquette functionality through binding of extremely hydrophobic cofactors to lipophilic domains

We demonstrate coordination of the extremely hydrophobic 13(2)-OH-Ni-bacteriochlorophyll (Ni-BChl) to the lipophilic domain of a novel, designed amphiphilic protein maquette (AP3) dispersed in detergent micelles [Discher et al. (2005) Biochemistry 44, 12329-12343]. Sedimentation velocity and equilibrium experiments and steady-state absorption spectra indicate that Ni-BChl-AP3 is a four-helix bundle containing one Ni-BChl axially ligated by one or two histidines. The nature of the ligation was pursued with ultrafast visible spectroscopy. While it is well established that light excitation of axially ligated mono- and bisimidazole Ni-BChl in solution leads to rapid imidazole dissociation and nanosecond recombination, there is no evidence of axial ligand dissociation in the light-excited Ni-BChl-AP3. This indicates that Ni-BChl is confined within the AP3 protein, ligated to histidines with severely restricted mobility. Dissociation constants show that Ni-BChl binding to AP3 is considerably weaker than the nanomolar range usual for heme and hydrophilic (HP) maquettes; moreover, there is a tendency for the Ni-BChl-AP3 four-helix bundles to dimerize into eight-helix bundles. Nevertheless, the preparation of the Ni-BChl-AP3 four-alpha-helix maquettes, supported by time-resolved spectroscopic analysis of the nature of the ligation, provides a viable new approach to AP maquette designs that address the challenges involved in binding extremely hydrophobic cofactors.

In situ determination of orientational distributions in Langmuir monolayers by total internal reflection fluorescence

A new application of the polarized total internal reflection fluorescence (PTIRF) technique to study the orientation distribution of a fluorophore within a Langmuir monolayer in situ on an aqueous subphase is described. The technique utilizes the measurement of polarized fluorescence, excited by the evanescent field appearing upon total internal reflection. The excitation by the evanescent field is achieved by launching the beam into a prism that is brought into contact with the monolayer from above. We also show here that a combination of PTIRF of monolayers on water and those freshly deposited onto the prism by horizontal lift in the same experiment provide enough data to determine the dielectric constant of the actual local environment of the fluorophore in the monolayer to eliminate the ambiguity of the orientation determination, arising from uncertainty in the normal component of excitation field. The new technique was applied to several model systems: fatty acid monolayers containing amphiphilic dyes DiI or BODIPY and also a monolayer of a synthetic amphiphilic porphyrin-binding peptide AP0. This technique is more accurate than polarized epifluorescence (PEF) in determining the fluorophore orientation distribution due to the much higher normal component of the excitation, achievable in the evanescent field, and to the lack of surface vibrations caused by capillary waves. Comparison of the new PTIRF approach with PEF shows that the monolayer structure is not disturbed by weak van der Waals attachment to the hydrophobic substrate.

Self-assembly of reactive amphiphilic block copolymers as mimetics for biological membranes

Over the years, polymers have attracted a great deal of interest because they offer a unique platform for the development of materials in fields as diverse as biomedicine and packaging. Many of these purposes use polymers that had been developed for totally different applications. Recently, however, chemical tailoring and molecular and supramolecular control of the chemistry and, thus, the physical and biological response have become a key interest of many researchers. In particular, systems that operate in aqueous media have become an intensely researched field. This is mostly because many devices must be biocompatible, which implies that they have to function in aqueous solutions. Over the past few years, new approaches for mimicking cell surfaces, for generating biocompatible and bioactive drug delivery systems, and for directed targeting have been developed. One recent development is polymeric systems with an enhanced biofunctionality, such as amphiphilic block copolymers that can act as mimetics for biological membranes. Because there are virtually no limits to combinations of monomers, biological and synthetic building blocks, ligands, receptors, and other proteins, polymer hybrid materials show a great promise for applications in biomedicine and biotechnology.

A model membrane protein for binding volatile anesthetics

Earlier work demonstrated that a water-soluble four-helix bundle protein designed with a cavity in its nonpolar core is capable of binding the volatile anesthetic halothane with near-physiological affinity (0.7 mM Kd). To create a more relevant, model membrane protein receptor for studying the physicochemical specificity of anesthetic binding, we have synthesized a new protein that builds on the anesthetic-binding, hydrophilic four-helix bundle and incorporates a hydrophobic domain capable of ion-channel activity, resulting in an amphiphilic four-helix bundle that forms stable monolayers at the air/water interface. The affinity of the cavity within the core of the bundle for volatile anesthetic binding is decreased by a factor of 4-3.1 mM Kd as compared to its water-soluble counterpart. Nevertheless, the absence of the cavity within the otherwise identical amphiphilic peptide significantly decreases its affinity for halothane similar to its water-soluble counterpart. Specular x-ray reflectivity shows that the amphiphilic protein orients vectorially in Langmuir monolayers at higher surface pressure with its long axis perpendicular to the interface, and that it possesses a length consistent with its design. This provides a successful starting template for probing the nature of the anesthetic-peptide interaction, as well as a potential model system in structure/function correlation for understanding the anesthetic binding mechanism.