Computational design of virus-like protein assemblies on carbon nanotube surfaces

Computational design and experimental characterization of peptides intended for pH-dependent membrane insertion and pore formation

There are many opportunities to use macromolecules, such as peptides and oligonucleotides, for intracellular applications. Despite this, general methods for delivering these molecules to the cytosol in a safe and efficient manner are not available. Efforts to develop a variety of intracellular drug delivery systems such as viral vectors, lipoplexes, nanoparticles, and amphiphilic peptides have been made, but various challenges such as delivery efficiency, toxicity, and controllability remain. A central challenge is the ability to selectively perturb, not destroy, the membrane to facilitate cargo introduction. Herein, we describe our efforts to design and characterize peptides that form pores inside membranes at acidic pH, so-called pH-switchable pore formation (PSPF) peptides, as a potential means for facilitating cargo translocation through membranes. Consistent with pore formation, these peptides exhibit low-pH-triggered selective release of ATP and miRNA, but not hemoglobin, from red blood cells. Consistent with these observations, biophysical studies (tryptophan fluorescence, circular dichroism, size-exclusion chromatography, analytical ultracentrifugation, and attenuated total reflectance Fourier transformed infrared spectroscopy) show that decreased pH destabilizes the PSPF peptides in aqueous systems while promoting their membrane insertion. Together, these results suggest that reduced pH drives insertion of PSPF peptides into membranes, leading to target-specific escape through a proposed pore formation mechanism.

Significant Improvement of Oxidase Activity through the Genetic Incorporation of a Redox-active Unnatural Amino Acid

Incorporation of 3-methoxytyrosine boosts the oxidase activity of the myoglobin model of oxidase, stressing the importance of the redox potential tuning of tyrosine.

While nature employs various covalent and non-covalent strategies to modulate tyrosine (Y) redox potential and pK_a in order to optimize enzyme activities, such approaches have not been systematically applied for the design of functional metalloproteins. Through the genetic incorporation of 3-methoxytyrosine (OMeY) into myoglobin, we replicated important features of cytochrome c oxidase (CcO) in this small soluble protein, which exhibits selective O₂ reduction activity while generating a small amount of reactive oxygen species (ROS). These results demonstrate that the electron donating ability of a tyrosine residue in the active site is important for CcO function. Moreover, we elucidated the structural basis for the genetic incorporation of OMeY into proteins by solving the X-ray structure of OMeY specific aminoacyl-tRNA synthetase complexed with OMeY.

Solubilization of single-walled carbon nanotubes using a peptide aptamer in water below the critical micelle concentration

The solubilizing ability of single-walled carbon nanotubes (SWCNTs) in water with several dispersants was investigated. Among the dispersants, including low-molecular-weight surfactants, peptides, DNA, and a water-soluble polymer, the peptide aptamer, A2 (IFRLSWGTYFS), exhibited the highest dispersion capability below the critical micelle concentration at a concentration of 0.02 w/v%. The dispersion of supernatant aqueous solution of SWCNTs containing aptamer A2 was essentially unchanged for several months after high-speed ultracentrifugation and gave rise to an efficient and stable dispersion of the SWCNTs in water. From the results of isothermal titration calorimetry and molecular dynamics simulations, the effective binding capability of A2 was due to π-π interaction between aromatic groups in the peptide aptamer and the side walls of SWCNTs. Interestingly, the peptide aptamer showed the possibility of diameter separation of semiconducting SWCNTs using a uniform density gradient ultracentrifuge. These phenomena are encouraging results toward an effective approach to the dispersion and separation of SWCNTs.

Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies

Thiscritical reviewpresents a detailed overview of the chemico-physical principles ruling the non-covalent association between proteins and fullerene, carbon nanotubes and graphene towards the creation of fascinating and innovative hybrid materials for biotechnological applications.

Metal–organic framework MIL-101(Cr) as a sorbent of porous membrane-protected micro-solid-phase extraction for the analysis of six phthalate esters from drinking water: a combination of experimental and computational study

An attractive MIL-101(Cr) material was synthesized and applied as a sorbent in μ-SPE device for the pre-concentration of PAEs in drinking water for the first time.

Peptide-induced affinity binding of carbonic anhydrase to carbon nanotubes

Although affinity binding between short chain peptides and carbon nanotube (CNT) has been reported, little is known for the study of proteins with CNT recognition and specific binding capabilities. Herein, carbonic anhydrase (CA) was functionalized via protein fusion with a single-walled carbon nanotube (SWNTs)-binding peptide, thereby forming a bioactive protein with high affinity binding capability. TEM and AFM analyses showed that the fusion CA could firmly coat to SWNTs with a surface coverage over 51%, while the enzyme maintained its catalytic activity. Structural analysis revealed that slight conformation changes were induced as a result of the fusion; however, the affinity binding of CA to the hydrophobic surface of SWNTs restored the native structure of the protein, with the conformation of the SWNT-bound CA largely resembling that of the native parent enzyme. Interfacial interactions between the fusion CA and SWNT were further investigated with Raman spectrometry and microscopic analysis. The results suggested that such peptide-induced CNT-protein binding allows the development of bioactive hybrid materials with the native structures of the protein moieties largely undisrupted.

Computationally assisted engineering of protein cages

A hybrid computational method incorporating topographic analysis of protein surfaces and free-energy calculations of protein-protein interactions in protein nanocages is described. This design strategy can be used to engineer protein cages for enhanced structural stability and assembly.

Rapid search for tertiary fragments reveals protein sequence-structure relationships

Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure-sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure.

Synthetic Biology: A Bridge between Artificial and Natural Cells

Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications.

High thermodynamic stability of parametrically designed helical bundles

We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.

Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures

Coiled coils are widespread protein domains comprising α-helices wound around each other in a regular fashion. Owing to their regularity, coiled-coil structures can be fully described by parametric equations. This in turn makes them an excellent model for studying sequence-structure relationships in proteins. Here, we used computational design to identify sequence features that determine the degree of helix axial rotation in four-helical homo-oligomeric antiparallel coiled coils. We designed 135,000 artificial sequences for a repertoire of backbone models representing all theoretically possible axial rotation states. Analysis of the designed sequences revealed features that precisely define the rotation of the helices. Based on these features we implemented a bioinformatic tool, which given a coiled-coil sequence, predicts the rotation of the helices in its structure. Moreover, we showed that another structural parameter, helix axial shift, is coupled to helix axial rotation and that dependence between these two parameters narrows the number of possible axial rotation states.

Cancer therapy using ultrahigh hydrophobic drug-loaded graphene derivatives

This study aimed to demonstrate that curcumin (Cur)-containing graphene composites have high anticancer activity. Specifically, graphene-derivatives were used as nanovectors for the delivery of the hydrophobic anticancer drug Cur based on pH dependence. Different Cur-graphene composites were prepared based on polar interactions between Cur and the number of oxygen-containing functional groups of respective starting materials. The degree of drug-loading was found to be increased by increasing the number of oxygen-containing functional groups in graphene-derivatives. We demonstrated a synergistic effect of Cur-graphene composites on cancer cell death (HCT 116) both in vitro and in vivo. As-prepared graphene quantum dot (GQD)-Cur composites contained the highest amount of Cur nano-particles and exhibited the best anticancer activity compared to the other composites including Cur alone at the same dose. This is the first example of synergistic chemotherapy using GQD-Cur composites simultaneous with superficial bioprobes for tumor imaging.

Interaction of single-stranded DNA with curved carbon nanotube is much stronger than with flat graphite

We used single molecule force spectroscopy to measure the force required to remove single-stranded DNA (ssDNA) homopolymers from single-walled carbon nanotubes (SWCNTs) deposited on methyl-terminated self-assembled monolayers (SAMs). The peeling forces obtained from these experiments are bimodal in distribution. The cluster of low forces corresponds to peeling from the SAM surface, while the cluster of high forces corresponds to peeling from the SWCNTs. Using a simple equilibrium model of the single molecule peeling process, we calculated the free energy of binding per nucleotide. We found that the free energy of ssDNA binding to hydrophobic SAMs decreases as poly(A) > poly(G) ≈ poly(T) > poly(C) (16.9 ± 0.1; 9.7 ± 0.1; 9.5 ± 0.1; 8.7 ± 0.1 kBT, per nucleotide). The free energy of ssDNA binding to SWCNT adsorbed on this SAM also decreases in the same order poly(A) > poly(G) > poly(T) > poly(C), but its magnitude is significantly greater than that of DNA-SAM binding energy (38.1 ± 0.2; 33.9 ± 0.1; 23.3 ± 0.1; 17.1 ± 0.1 kBT, per nucleotide). An unexpected finding is that binding strength of ssDNA to the curved SWCNTs is much greater than to flat graphite, which also has a different ranking (poly(T) > poly(A) > poly(G) ≥ poly(C); 11.3 ± 0.8, 9.9 ± 0.5, 8.3 ± 0.2, and 7.5 ± 0.8 kBT, respectively, per nucleotide). Replica-exchange molecular dynamics simulations show that ssDNA binds preferentially to the curved SWCNT surface, leading us to conclude that the differences in ssDNA binding between graphite and nanotubes arise from the spontaneous curvature of ssDNA.

Design and self-assembly of simple coat proteins for artificial viruses

Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing artificial life. Moreover, they are used in biomedical and biotechnological applications, such as targeted delivery of nucleic acids for gene therapy and as scaffolds in material science. In a natural setting, survival of viruses requires that a significant fraction of the replicated genomes be completely protected by coat proteins. Complete protection of the genome is ensured by a highly cooperative supramolecular process between the coat proteins and the nucleic acids, which is based on reversible, weak and allosteric interactions only. However, incorporating this type of supramolecular cooperativity into artificial viruses remains challenging. Here, we report a rational design for a self-assembling minimal viral coat protein based on simple polypeptide domains. Our coat protein features precise control over the cooperativity of its self-assembly with single DNA molecules to finally form rod-shaped virus-like particles. We confirm the validity of our design principles by showing that the kinetics of self-assembly of our virus-like particles follows a previous model developed for tobacco mosaic virus. We show that our virus-like particles protect DNA against enzymatic degradation and transfect cells with considerable efficiency, making them promising delivery vehicles.

A real-time all-atom structural search engine for proteins

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

DNA-controlled partition of carbon nanotubes in polymer aqueous two-phase systems

Sorting single-wall carbon nanotubes (SWCNTs) of different chiralities is both scientifically interesting and technologically important. Recent studies have shown that polymer aqueous two-phase extraction is a very effective way to achieve nanotube sorting. However, works published to date have demonstrated only separation of surfactant-dispersed SWCNTs, and the mechanism of chirality-dependent SWCNT partition is not well understood. Here we report a systematic study of spontaneous partition of DNA-wrapped SWCNTs in several polymer aqueous two-phase systems. We show that partition of DNA-SWCNT hybrids in a given polymer two-phase system is strongly sequence-dependent and can be further modulated by salt and polymer additives. With the proper combination of DNA sequence, polymer two-phase system, and partition modulators, as many as 15 single-chirality nanotube species have been effectively purified from a synthetic mixture. As an attempt to provide a unified partition mechanism of SWCNTs dispersed by surfactants and by DNA, we present a qualitative analysis of solvation energy for SWCNT colloids in a polymer-modified aqueous phase. Our observation and analysis highlight the sensitive dependence of the hydration energy on the spatial distribution of hydrophilic functionalities.

Host-guest nanocomposites of multiwalled carbon nanotubes and ionic liquids with controllable composition

It is widely believed that low-volatility is a defining characteristic of ionic liquids (ILs). Here we synthesize a series of host-guest nanocomposites containing multiwalled carbon nanotubes (MWCNTs) and ILs using the volatility of ILs under vacuum conditions. The nanocomposites with different IL contents can be easily obtained through simple physical methods. The interactions between IL and MWCNTs are thoroughly investigated. This new nanocomposite can be used both in carbon catalysis and IL catalysis.

Accurate design of co-assembling multi-component protein nanomaterials

The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.

C60@Lysozyme: direct observation by nuclear magnetic resonance of a 1:1 fullerene protein adduct

Integrating carbon nanoparticles (CNPs) with proteins to form hybrid functional assemblies is an innovative research area with great promise for medical, nanotechnology, and materials science. The comprehension of CNP-protein interactions requires the still-missing identification and characterization of the 'binding pocket' for the CNPs. Here, using Lysozyme and C60 as model systems and NMR chemical shift perturbation analysis, a protein-CNP binding pocket is identified unambiguously in solution and the effect of the binding, at the level of the single amino acid, is characterized by a variety of experimental and computational approaches. Lysozyme forms a stoichiometric 1:1 adduct with C60 that is dispersed monomolecularly in water. Lysozyme maintains its tridimensional structure upon interaction with C60 and only a few identified residues are perturbed. The C60 recognition is highly specific and localized in a well-defined pocket.

Structural Stability and Binding Strength of a Designed Peptide-Carbon Nanotube Hybrid

Biological polymers hybridized with single-walled carbon nanotubes (SWCNTs) have elicited much interest recently for applications in SWCNT-based sorting as well as biomedical imaging, sensing, and drug delivery. Recently, de novo designed peptides forming a coiled-coil structure have been engineered to selectively disperse SWCNT of a certain diameter. Here we report on a study of the binding strength and structural stability of the hybrid between such a "HexCoil-Ala" peptide and the (6,5)-SWCNT. Using the competitive binding of a surfactant, we find that affinity strength of the peptide ranks in comparison to that of two single-stranded DNA sequences as (GT)₃₀-DNA > HexCoil-Ala > (TAT)₄T-DNA. Further, using replica exchange molecular dynamics (REMD), we show that the hexamer peptide complex has both similarities with and differences from the original design. While one of two distinct helix-helix interfaces of the original model was largely retained, a second interface showed much greater variability. These conformational differences allowed an aromatic tyrosine residue designed to lie along the solvent-exposed surface of the protein instead to penetrate between the two helices and directly contact the SWCNT. These insights will inform future designs of SWCNT-interacting peptides.

The devil and holy water: protein and carbon nanotube hybrids

Integrating carbon nanotubes (CNTs) with biological systems to form hybrid functional assemblies is an innovative research area with great promise for medical, nanotechnology, and materials science applications. The specifics of molecular recognition and catalytic activity of proteins combined with the mechanical and electronic properties of CNTs provides opportunities for physicists, chemists, biologists, and materials scientists to understand and develop new nanomachines, sensors, or any of a number of other molecular assemblies. Researchers know relatively little about the structure, function, and spatial orientation of proteins noncovalently adsorbed on CNTs, yet because the interaction of CNTs with proteins depends strongly on the tridimensional structure of the proteins, many of these questions can be answered in simple terms. In this Account, we describe recent research investigating the properties of CNT/protein hybrids. Proteins act to solvate CNTs and may sort them according to diameter or chirality. In turn, CNTs can support and immobilize enzymes, creating functional materials. Additional applications include proteins that assemble ordered hierarchical objects containing CNTs, and CNTs that act as protein carriers for vaccines, for example. Protein/CNT hybrids can form bioscaffolds and can serve as therapeutic and imaging materials. Proteins can detect CNTs or coat them to make them biocompatible. One of the more challenging applications for protein/CNT hybrids is to make CNT substrates for cell growth and neural interfacing applications. The challenge arises from the structures' interactions with living cells, which poses questions surrounding the (nano)toxicology of CNTs and whether and how CNTs can detect biological processes or sense them as they occur. The surface chemistry of CNTs and proteins, including interactions such as π-π stacking interactions, hydrophobic interactions, surfactant-like interactions, and charge-π interactions, governs the wealth of structures, processes, and functions that appear when such different types of molecules interact. Each residue stars in one of two main roles, and understanding which residues are best suited for which type of interaction can lead to the design of new hybrids. Nonlocally, the peptide or protein primary, secondary, and tertiary structures govern the binding of proteins by CNTs. The conjugation of proteins with CNTs presents some serious difficulties both experimentally and culturally (such as bridging the "jargon barrier" across disciplines). The intersection of these fields lies between communities characterized by distinctly different approaches and methodologies. However, the examples of this Account illustrate that when this barrier is overcome, the exploitation of hybrid CNT-protein systems offers great potential.

New designed protein assemblies

Self-assembly is an essential concept of all organisms. Polypeptides self-assemble either within a single polypeptide chain or through assembly of protein domains. Recent advances in designed protein assemblies were achieved by genetic or chemical linkage of oligomerization domains and by engineering new interaction interfaces, which resulted in formation of lattices and cage-like protein assemblies. The absence of new experimentally determined protein folds in the last few years underlines the challenge of designing new folds. Recently a new strategy for designing self-assembly of a polypeptide fold, based on the topological arrangement of coiled-coil modules as the protein origami, has been proposed. The polypeptide tetrahedron was designed from a single chain concatenating of coiled-coil forming building modules interspersed with flexible hinges. In this strategy the order of coiled-coil segments defines the fold of the polypeptide nanostructure.

Nanotubes complexed with DNA and proteins for resistive-pulse sensing

We use a resistive-pulse technique to analyze molecular hybrids of single-wall carbon nanotubes (SWNTs) wrapped in either single-stranded DNA or protein. Electric fields confined in a glass capillary nanopore allow us to probe the physical size and surface properties of molecular hybrids at the single-molecule level. We find that the translocation duration of a macromolecular hybrid is determined by its hydrodynamic size and solution mobility. The event current reveals the effects of ion exclusion by the rod-shaped hybrids and possible effects due to temporary polarization of the SWNT core. Our results pave the way to direct sensing of small DNA or protein molecules in a large unmodified solid-state nanopore by using nanofilaments as carriers.

Absolute free energies of biomolecules from unperturbed ensembles

Computing the absolute free energy of a macromolecule's structural state, F, is a challenging problem of high relevance. This study presents a method that computes F using only information from an unperturbed simulation of the macromolecule in the relevant conformational state, ensemble, and environment. Absolute free energies produced by this method, dubbed Valuation of Local Configuration Integral with Dynamics (VALOCIDY), enable comparison of alternative states. For example, comparing explicitly solvated and vaporous states of amino acid side-chain analogs produces solvation free energies in good agreement with experiments. Also, comparisons between alternative conformational states of model heptapeptides (including the unfolded state) produce free energy differences in agreement with data from μs molecular-dynamics simulations and experimental propensities. The potential of using VALOCIDY in computational protein design is explored via a small design problem of stabilizing a β-turn structure. When VALOCIDY-based estimation of folding free energy is used as the design metric, the resulting sequence folds into the desired structure within the atomistic force field used in design. The VALOCIDY-based approach also recognizes the distinct status of the native sequence regardless of minor details of the starting template structure, in stark contrast with a traditional fixed-backbone approach.

Engineering a well-ordered, functional protein-gold nanoparticle assembly

The study of interactions between proteins and nanoparticles is important to advancing applications of nanoparticles in biology, medicine, and materials science. Here, we report the encapsulation of a 5-nm diameter gold nanoparticle (AuNP) by thermophilic ferritin (tF), achieved in nearly quantitative yield under mild conditions that preserved the secondary structure, ferroxidase activity, and thermal stability of the native, 4-helix bundle protein subunits. Chromatography-based assays determined that stable protein assembly around AuNPs occurred on long time scales (~48h) and was reversible. Apparent association constants were determined at 25°C for equilibrated tF-BSPP-capped AuNP samples (KA=(2.1±0.4)×10(78)M(-11)) and compared favorably to salt-assembled tF samples (KA=(2.2±0.5)×10(68)M(-11)) at the same protein concentration (0.3mg/mL). Finally, addition of gold ions and mild reducing agent to the tF-AuNP assembly produced 8-nm diameter AuNPs with surface plasmon resonance band unchanged at 520nm, indicative of templating by the protein shell.

Surface-induced conformational and functional changes of bone morphogenetic protein-2 adsorbed onto single-walled carbon nanotubes

Efficient immobilization of bone morphogenetic protein-2 (BMP-2) onto matrix is of crucial importance in the development of BMP-2-based bone tissue scaffold/implant. This often ties with precise control of desirable protein conformation and retention of protein activity. Recently, great attentions were paid to the regulation of protein conformation by tailoring the nanoscale surface properties. In this contribution, with hydrophilic COOH- and hydrophobic CH3-terminated single-walled carbon nanotubes (SWNTs-COOH and SWNTs-CH3) as models, we investigated the nanoscale interface-induced changes of adsorption dynamics, conformation, and bioactivity of recombinant human BMP-2 (rhBMP-2). Our data showed that SWNTs-COOH and SWNTs-CH3 bound rapidly to and induced unfolding of rhBMP-2 molecules, which promoted their interactions with corresponding receptors on cell surface and thus enhanced their bioactivities. In contrast, rhBMP-2 showed stronger affinity to the COOH-terminated surface than that terminated with CH3 groups, while better enhanced bioactivity on the SWNTs-CH3 surfaces. After released from SWNTs, the unfolded rhBMP-2 refolded and their activities from SWNTs-COOH and SWNTs-CH3 were reduced to 90% and 70% of the native rhBMP-2, respectively. Based on these results obtained, a model of the binding characteristics of rhBMP-2 onto SWNTs with different chemistry is presented. This study demonstrates the possibility of simple tailor-made nanoscale chemical surfaces to modulate the binding, conformation and bioactivity of BMP-2, allowing fabrication of BMP-2-based bone tissue scaffolds with high osteoinductivity and low BMP-2 dosage.

Assembling an ion channel: ORF 3a from SARS-CoV

Protein 3a is a 274 amino acid polytopic channel protein with three putative transmembrane domains (TMDs) encoded by severe acute respiratory syndrome corona virus (SARS-CoV). Synthetic peptides corresponding to each of its three individual transmembrane domains (TMDs) are reconstituted into artificial lipid bilayers. Only TMD2 and TMD3 induce channel activity. Reconstitution of the peptides as TMD1 + TMD3 as well as TMD2 + TMD3 in a 1 : 1 mixture induces membrane activity for both mixtures. In a 1 : 1 : 1 mixture, channel like behavior is almost restored. Expression of full length 3a and reconstitution into artificial lipid bilayers reveal a weak cation selective (PK ≈ 2 PCl ) rectifying channel. In the presence of nonphysiological concentration of Ca-ions the channel develops channel activity.

Chameleon-like self-assembling peptides for adaptable biorecognition nanohybrids

We present here the development of adaptable hybrid materials in which self-assembling peptides can sense the diameter/curvature of carbon nanotubes and then adjust their overall structures from disordered states to α-helices, and vice versa. The peptides within the hybrid materials show exceptionally high thermal-induced conformational stability and molecular recognition capability for target RNA. This study shows that the context-dependent protein-folding effects can be realized in artificial nanosystems and provides a proof of principle that nanohybrid materials decorated with structured and adjustable peptide units can be fabricated using our strategy, from which smart and responsive organic/inorganic hybrid materials capable of sensing and controlling diverse biological molecular recognition events can be developed.

Computational protein design: the Proteus software and selected applications

We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated command language, supporting several force fields and solvent models. A second program provides algorithms to search sequence space. It allows a decomposition of the system into groups, which can be combined in different ways in the energy function, for both positive and negative design. The whole procedure can be controlled by editing 2-4 scripts. Two applications consider the tyrosyl-tRNA synthetase enzyme and its successful redesign to bind both O-methyl-tyrosine and D-tyrosine. For the latter, we present Monte Carlo simulations where the D-tyrosine concentration is gradually increased, displacing L-tyrosine from the binding pocket and yielding the binding free energy difference, in good agreement with experiment. Complete redesign of the Crk SH3 domain is presented. The top 10000 sequences are all assigned to the correct fold by the SUPERFAMILY library of Hidden Markov Models. Finally, we report the acid/base behavior of the SNase protein. Sidechain protonation is treated as a form of mutation; it is then straightforward to perform constant-pH Monte Carlo simulations, which yield good agreement with experiment. Overall, the software can be used for a wide range of application, producing not only native-like sequences but also thermodynamic properties with errors that appear comparable to other current software packages.

Strategies to control the binding mode of de novo designed protein interactions

There has been significant recent progress in the computational design of protein interactions including the creation of novel heterodimers, homodimers, nanohedra, fibril caps and a protein crystal. Essential to these successes has been the use of innovative strategies for finding binding modes that are achievable, that is, identifying binding partners and docked conformations that can be successfully stabilized via sequence optimization and backbone refinement. In many cases this has involved the use of structural motifs commonly found at naturally occurring interfaces including alpha helices inserted into hydrophobic grooves, beta-strand pairing, metal binding, established helix packing motifs, and the use of symmetry to form cooperative interactions. Future challenges include the creation of hydrogen bond networks and antibody-like interactions based on the redesign of protein surface loops.

Practical approaches to designing novel protein assemblies

Molecular self-assembly offers a means by which sophisticated materials can be constructed with unparalleled precision. Designing self-assembling protein structures is of particular interest as a result of the unique functional capabilities of proteins. Custom-designed protein materials could lead to new possibilities in therapeutics, bioenergy, and materials science. Although the field was long hampered by the challenges involved in designing such complex molecules, novel approaches and computational tools have recently led to remarkable progress. Here we review recent design studies in the context of three fundamental aspects of self-assembling materials: subunit organization, subunit interactions, and regulation of assembly.

Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding

We computationally designed a de novo protein-protein interaction between wild-type ubiquitin and a redesigned scaffold. Our strategy was to incorporate zinc at the designed interface to promote affinity and orientation specificity. A large set of monomeric scaffold surfaces were computationally engineered with three-residue zinc coordination sites, and the ubiquitin residue H68 was docked to the open coordination site to complete a tetrahedral zinc site. This single coordination bond was intended as a hotspot and polar interaction for ubiquitin binding, and surrounding residues on the scaffold were optimized primarily as hydrophobic residues using a rotamer-based sequence design protocol in Rosetta. From thousands of independent design simulations, four sequences were selected for experimental characterization. The best performing design, called Spelter, binds tightly to zinc (Kd  < 10 nM) and binds ubiquitin with a Kd of 20 µM in the presence of zinc and 68 µM in the absence of zinc. Mutagenesis studies and nuclear magnetic resonance chemical shift perturbation experiments indicate that Spelter interacts with H68 and the target surface on ubiquitin; however, H68 does not form a hotspot as intended. Instead, mutation of H68 to alanine results in tighter binding. Although a 3/1 zinc coordination arrangement at an interface cannot be ruled out as a means to improve affinity, our study led us to conclude that 2/2 coordination arrangements or multiple-zinc designs are more likely to promote high-affinity protein interactions.

Computational enzyme design

Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.

Tunable carbon nanotube/protein core-shell nanoparticles with NIR- and enzymatic-responsive cytotoxicity

A unique procedure is developed to capture carbon nanotubes into closed virus-like protein cages with a controllable shell. The cross-linked shell varies in thickness within ≈10(0) -10(2) nm, and can be entirely removed by enzyme degradation. The cytotoxicity is entirely suppressed, but can be promoted again by enzymes and near-infrared light. These hybrids can be decorated with functional inorganic nanoparticles or processed into nanocomposites.

Mining tertiary structural motifs for assessment of designability

The observation of a limited secondary-structural alphabet in native proteins, with significant sequence preferences, has profoundly influenced the fields of protein design and structure prediction (Simons, Kooperberg, Huang, & Baker, 1997; Verschueren et al., 2011). In the era of structural genomics, as the size of the structural dataset continues to grow rapidly, it is becoming possible to extend this analysis to tertiary structural motifs and their sequences. For a hypothetical tertiary motif, the rate of its utilization in natural proteins may be used to assess its designability-the ease with which the motif can be realized with natural amino acids. This requires a structural similarity search methodology, which rather than looking for global topological agreement (more appropriate for categorization of full proteins or domains), identifies detailed geometric matches. In this chapter, we introduce such a method, called MaDCaT, and demonstrate its use by assessing the designability landscapes of two tertiary structural motifs. We also show that such analysis can establish structure/sequence links by providing the sequence constraints necessary to encode designable motifs. As logical extension of their secondary-structure counterparts, tertiary structural preferences will likely prove extremely useful in de novo protein design and structure prediction.

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (K_d), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.