A hierarchic approach to the design of hexameric helical barrels

De novo protein design, a retrospective

Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.

Rational design of a hexameric protein assembly stabilized by metal chelation

Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)₃ complexes. The assemblies are stable to thermal denaturation, and are more than 90% helical at 90°C. Circular dichroism spectroscopy shows that one of the 2 possible (Bpy)₃ enantiomers is favored over the other. Because of the sequence pliability of the starting peptides, these constructs could find use to organize functional groups at controlled positions within a supramolecular assembly.

Coiled-Coil Design: Updated and Upgraded

α-Helical coiled coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural coiled-coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple coiled coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers. In turn, these provide a toolkit for directing the assembly of both natural proteins and more complex designs in protein engineering, materials science and synthetic biology. Moving on, the increased and improved use of computational design is allowing access to coiled-coil structures that are rare or even not observed in nature, for example α-helical barrels, which comprise five or more α-helices and have central channels into which different functions may be ported. This chapter reviews all of these advances, outlining improvements in our knowledge of the fundamentals of coiled-coil folding and assembly, and highlighting new coiled coil-based materials and applications that this new understanding is opening up. Despite considerable progress, however, challenges remain in coiled-coil design, and the next decade promises to be as productive and exciting as the last.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel β-sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac12 c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac12 c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C(α,α) -dialkylated residue Ac12 c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel β-sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac12 c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel β-sheet in crystals, twisted or helical β-sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted β-sheet assembly in crystals.

Modulation of cluster incorporation specificity in a de novo iron-sulfur cluster binding peptide

iron-sulfur cluster binding proteins perform an astounding variety of functions, and represent one of the most abundant classes of metalloproteins. Most often, they constitute pairs or chains and act as electron transfer modules either within complex redox enzymes or within small diffusible proteins. We have previously described the design of a three-helix bundle that can bind two clusters within its hydrophobic core. Here, we use single-point mutations to exchange one of the Cys ligands coordinating the cluster to either Leu or Ser. We show that the mutants modulate the redox potential of the clusters and stabilize the [3Fe-4S] form over the [4Fe-4S] form, supporting the use of model iron-sulfur cluster proteins as modules in the design of complex redox enzymes.

Computational design of a protein crystal

Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a "honeycomb-like" structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify "designable" structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.

A de novo peptide hexamer with a mutable channel

The design of new proteins that expand the repertoire of natural protein structures represents a formidable challenge. Success in this area would increase understanding of protein structure, and present new scaffolds that could be exploited in biotechnology and synthetic biology. Here we describe the design, characterisation and X-ray crystal structure of a new coiled-coil protein. The de novo sequence forms a stand-alone, parallel, 6-helix bundle with a channel running through it. Although lined exclusively by hydrophobic leucine and isoleucine side chains, the 6 Å channel is permeable to water. One layer of leucine residues within the channel is mutable accepting polar aspartic acid (Asp) and histidine (His) side chains, and leading to subdivision and organization of solvent within the lumen. Moreover, these mutants can be combined to form a stable and unique (Asp-His)₃ heterohexamer. These new structures provide a basis for engineering de novo proteins with new functions.

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

There is a general need for the engineering of protein-like molecules that organize into geometrically specific superstructures on molecular surfaces, directing further functionalization to create richly textured, multilayered assemblies. Here we describe a computational approach whereby the surface properties and symmetry of a targeted surface define the sequence and superstructure of surface-organizing peptides. Computational design proceeds in a series of steps that encode both surface recognition and favorable intersubunit packing interactions. This procedure is exemplified in the design of peptides that assemble into a tubular structure surrounding single-walled carbon nanotubes (SWNTs). The geometrically defined, virus-like coating created by these peptides converts the smooth surfaces of SWNTs into highly textured assemblies with long-scale order, capable of directing the assembly of gold nanoparticles into helical arrays along the SWNT axis.

A polypeptide "building block" for the β-trefoil fold identified by "top-down symmetric deconstruction"

Fibroblast growth factor-1, a member of the 3-fold symmetric β-trefoil fold, was subjected to a series of symmetric constraint mutations in a process termed "top-down symmetric deconstruction." The mutations enforced a cumulative exact 3-fold symmetry upon symmetrically equivalent positions within the protein and were combined with a stability screen. This process culminated in a β-trefoil protein with exact 3-fold primary-structure symmetry that exhibited excellent folding and stability properties. Subsequent fragmentation of the repeating primary-structure motif yielded a 42-residue polypeptide capable of spontaneous assembly as a homotrimer, producing a thermostable β-trefoil architecture. The results show that despite pronounced reduction in sequence complexity, pure symmetry in the design of a foldable, thermostable β-trefoil fold is possible. The top-down symmetric deconstruction approach provides a novel alternative means to successfully identify a useful polypeptide "building block" for subsequent "bottom-up" de novo design of target protein architecture.

Bipartite design of a self-fibrillating protein copolymer with nanopatterned peptide display capabilities

The development of biomatrices for technological and biomedical applications employs self-assembled scaffolds built from short peptidic motifs. However, biopolymers composed of protein domains would offer more varied molecular frames to introduce finer and more complex functionalities in bioreactive scaffolds using bottom-up approaches. Yet, the rules governing the three-dimensional organization of protein architectures in nature are complex and poorly understood. As a result, the synthetic fabrication of ordered protein association into polymers poses major challenges to bioengineering. We have now fabricated a self-assembling protein nanofiber with predictable morphologies and amenable to bottom-up customization, where features supporting function and assembly are spatially segregated. The design was inspired by the cross-linking of titin filaments by telethonin in the muscle sarcomere. The resulting fiber is a two-protein system that has nanopatterned peptide display capabilities as shown by the recruitment of functionalized gold nanoparticles at regular intervals of ∼ 5 nm, yielding a semiregular linear array over micrometers. This polymer promises the uncomplicated display of biologically active motifs to selectively bind and organize matter in the fine nanoscale. Further, its conceptual design has high potential for controlled plurifunctionalization.

Infrared signature and folding dynamics of a helical beta-peptide

Synthetic foldamers consisting of beta-amino acids offer excellent model systems for examining the effect of backbone flexibility on the dynamics of protein folding. Herein, we study the folding-unfolding kinetics of a beta-peptide that folds into a 14-helical structure in water. We find that the T-jump induced relaxation kinetics of this peptide occur on the nanosecond time scale and are noticeably slower than those of alanine-based alpha-helical peptides, and additionally, the relaxation rates show a weaker dependence on temperature. These differences appear to indicate that the folding energy landscapes of these peptides are different. In addition, we find that the amide I' band of this beta-peptide exhibits a sharp feature at approximately 1612 cm(-1), which we believe is a distinct infrared reporter of 14-helix.

A superprotein triangle driven by nickel(II) coordination: exploiting non-natural metal ligands in protein self-assembly

We previously devised a strategy (metal-directed protein self-assembly, MDPSA) that utilizes the simultaneous stability, lability, and directionality of metal-ligand bonds to drive protein-protein interactions. Here we show that both the structural and functional scopes of MDPSA can be broadened by incorporation of non-natural metal-chelating ligands onto protein surfaces. A cytochrome cb(562) variant, MBP-Phen1, which features a covalently attached phenanthroline (Phen) group on its surface, self-assembles into an unusual triangular architecture (Ni(3):MBP-Phen1(3)) upon binding Ni as a result of specific Phen-protein interactions. The crystal structure of Ni(3):MBP-Phen1(3) reveals that the Phen group is buried in a small pocket on the protein surface, which results in an unsaturated Ni coordination environment.

Control of protein oligomerization symmetry by metal coordination: C2 and C3 symmetrical assemblies through Cu(II) and Ni(II) coordination

We describe the metal-dependent self-assembly of symmetrical protein homooligomers from protein building blocks that feature appropriately engineered metal-chelating motifs on their surfaces. Crystallographic studies indicate that the same four-helix-bundle protein construct, MBPC-1, can self-assemble into C(2) and C(3) symmetrical assemblies dictated by Cu(II) and Ni(II) coordination, respectively. The symmetry inherent in metal coordination can thus be directly applied to biological self-assembly.

Crystal structure of a self-assembling lipopeptide detergent at 1.20 A

Lipopeptide detergents (LPDs) are a new class of amphiphile designed specifically for the structural study of integral membrane proteins. The LPD monomer consists of a 25-residue peptide with fatty acyl chains linked to side chains located at positions 2 and 24 of the peptide. LPDs are designed to form alpha-helices that self-assemble into cylindrical micelles, providing a more natural interior acyl chain packing environment relative to traditional detergents. We have determined the crystal structure of LPD-12, an LPD coupled to two dodecanoic acids, to a resolution of 1.20 A. The LPD-12 monomers adopt the target conformation and associate into cylindrical octamers as expected. Pairs of helices are strongly associated as Alacoil-type antiparallel dimers, and four of these dimers interact through much looser contacts into assemblies with approximate D(2) symmetry. The aligned helices form a cylindrical shell with a hydrophilic exterior that protects an interior hydrophobic cavity containing the 16 LPD acyl chains. Over 90% of the methylene/methyl groups from the acylated side chains are visible in the micelle interiors, and approximately 90% of these adopt trans dihedral angle conformations. Dodecylmaltoside (DDM) was required for the crystallization of LPD-12, and we find 10-24 ordered DDM molecules associated with each LPD assembly, resulting in an overall micelle molecular weight of approximately 30 kDa. The structures confirm the major design objectives of the LPD framework, and reveal unexpected features that will be helpful in the engineering additional versions of lipopeptide amphiphiles.

Assessing the integrity of designed homomeric parallel three-stranded coiled coils in the presence of metal ions

De novo design of alpha-helical peptides that self-assemble to form helical coiled coils is a powerful tool for studying molecular recognition between peptides/proteins and determining the fundamental forces involved in their folding and structure. These amphipathic helices assemble in aqueous solution to generate the final coiled coil motif, with the hydrophobic residues in the interior and the polar/hydrophilic groups on the exterior. Considerable effort has been devoted to investigate the forces that determine the overall stability and final three-dimensional structure of the coiled coils. One of the major challenges in coiled coil design is the achievement of specificity in terms of the oligomeric state, with respect to number (two, three, four, or higher), nature (homomers vs heteromers), and strand orientation (parallel vs antiparallel). As seen in nature, metal ions play an important role in this self-organization process, and the overall structure of metalloproteins is primarily the result of two driving forces: the metal coordination preference and the fold of the polypeptide backbone. Previous work in our group has shown that metal ions such as As(III) and Hg(II) can be used to enforce different aggregation states in the Cys derivatives of the designed homotrimeric coiled-coil TRI family [Ac-G(LKALEEK)4G-CONH2]. We are now interested in studying the interplay between the metal ion and peptide preferences in controlling the specificity and relative orientation of the alpha-helices in coiled coils. For this objective, two derivatives of the TRI family, TRi L2WL9C and TRi L2WL23C, have been synthesized. Along with those two peptides, two derivatives of Coil-Ser, CSL9C and CSL19C (CS = Ac-EWEALEKKLAALESKLQALEKKLEALEHG-CONH2), a similar de novo designed three-stranded coiled coil that has the potential to form antiparallel coiled coils, have also been used. Circular dichroism, UV-vis, and 199Hg and 113Cd NMR spectroscopy results reveal that the addition of Hg(II) and Cd(II) to the different mixtures of these peptides forms preferentially homotrimeric coiled coils, over a statistical population of heterotrimeric parallel and antiparallel coiled coils.

Analysis of peptide design in four-, five-, and six-helix bundle template assembled synthetic protein molecules

Four-, five-, and six-helix bundle template assembled synthetic proteins (TASPs) have been synthesized using disulfide bonds between cavitand templates and peptides, and characterized in terms of stability and structural specificity. The peptide sequence (CGGGEELLKKLEE LLKKG) used was originally designed for a four-helix bundle. The TASPs were analyzed using CD spectroscopy, chemical denaturation studies, NMR spectroscopy, sedimentation equilibria studies, and hydrophobic dye binding studies to determine the effect of a single peptide sequence when incorporated into bundles with different numbers of helices. If the design was indeed idealized for a four-helix bundle, then the five- and six-helix bundles should be less stable and manifest lower conformational specificity. The TASPs all demonstrated high stability and cooperative unfolding. However, the four-helix bundle was found to be significantly more stable and nativelike compared to the five- and six-helix bundles. This suggests that the peptide sequence is specific to the four-helix bundle, as designed. This result demonstrates the ability to design de novo proteins with specified structure, not just generic stability.

Characterization of de novo four-helix bundles by molecular dynamics simulations

We have investigated the structure and dynamics of three cavitand-based four-helix bundles (caviteins) by computer simulation. In these systems, designed de novo, each of the four helices contain the identical basis sequence EELLKKLEELLKKG (N1). Each cavitein consists of a rigid macrocycle (cavitand) with four aryl linkages, to each of which is connected an N1 peptide by means of a linker peptide. The three caviteins studied here differ only in the linker peptide, which consist of one, two, or three glycine residues. Previous experimental work has shown that these systems exhibit very different behavior in terms of stability and oligomerization states despite the small differences in the linker peptide. Given that to date no three-dimensional structure is available for these caviteins, we have undertaken a series of molecular dynamics (MD) simulations in explicit water to try to rationalize the large differences in the experimentally observed behavior of these systems. Our results provide insight, for the first time, into why and how the cavitein with a single glycine linker forms dimers. In addition, our results indicate why although the two- and three-glycine-linked caviteins have similar stabilities, they have different native-like characteristics: the cavitein with three glycines can form a supercoiled helix, whereas the one with two glycines cannot. These findings may provide a useful guide in the rational de novo design of novel proteins with finely tunable structures and functions in the future.

A designed well-folded monomeric four-helix bundle protein prepared by Fmoc solid-phase peptide synthesis and native chemical ligation

The design and total chemical synthesis of a monomeric native-like four-helix bundle protein is presented. The designed protein, GTD-Lig, consists of 90 amino acids and is based on the dimeric structure of the de novo designed helix-loop-helix GTD-43. GTD-Lig was prepared by the native chemical ligation strategy and the fragments (45 residues long) were synthesized by applying standard fluorenylmethoxycarbonyl (Fmoc) chemistry. The required peptide-thioester fragment was prepared by anchoring the free gamma-carboxy group of Fmoc-Glu-allyl to the solid phase. After chain elongation the allyl moiety was orthogonally removed and the resulting carboxy group was functionalized with a glycine-thioester followed by standard trifluoroacetic acid (TFA) cleavage to produce the unprotected peptide-thioester. The structure of the synthetic protein was examined by far- and near-UV circular dichroism (CD), sedimentation equilibrium ultracentrifugation, and NMR and fluorescence spectroscopy. The spectroscopic methods show a highly helical and native-like monomeric protein consistent with the design. Heat-induced unfolding was studied by tryptophan absorbance and far-UV CD. The thermal unfolding of GTD-Lig occurs in two steps; a cooperative transition from the native state to an intermediate state and thereafter by noncooperative melting to the unfolded state. The intermediate exhibits the properties of a molten globule such as a retained native secondary structure and a compact hydrophobic core. The thermodynamics of GuHCl-induced unfolding were evaluated by far-UV CD monitoring and the unfolding exhibited a cooperative transition that is well-fitted by a two-state mechanism from the native to the unfolded state. GTD-Lig clearly shows the characteristics of a native protein with a well-defined structure and typical unfolding transitions. The design and synthesis presented herein is of general applicability for the construction of large monomeric proteins.

Protein oligomerization: how and why

A large fraction of cellular proteins are oligomeric. Protein oligomerization may often be an advantageous feature from the perspective of protein evolution and has probably evolved by a variety of mechanisms. The study of protein oligomerization may provide insights into the early protein environment and the evolution of modern proteins. Oligomeric mini-proteins, short peptides with discrete protein-like structures, may serve as valuable models for understanding features of protein oligomerization.

Synthetic biology

Synthetic biologists come in two broad classes. One uses unnatural molecules to reproduce emergent behaviours from natural biology, with the goal of creating artificial life. The other seeks interchangeable parts from natural biology to assemble into systems that function unnaturally. Either way, a synthetic goal forces scientists to cross uncharted ground to encounter and solve problems that are not easily encountered through analysis. This drives the emergence of new paradigms in ways that analysis cannot easily do. Synthetic biology has generated diagnostic tools that improve the care of patients with infectious diseases, as well as devices that oscillate, creep and play tic-tac-toe.

Stabilization of the fibrous structure of an α-helix-forming peptide by sequence reversal

The alpha3-peptide, which comprises three repeats of the sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala and forms an amphipathic alpha-helix, is unique among various alpha-helix-forming peptides in that it assembles into fibrous structures that can be observed by transmission electron microscopy. As part of our investigation of the structure-stability relationships of the alpha3-peptide, we synthesized the r3-peptide, whose amino acid sequence is the reverse of that of the alpha3-peptide, and we investigated the effects of sequence reversal on alpha-helix stability and the formation of fibrous structures. Unexpectedly, the r3-peptide formed a more-stable alpha-helix and longer fibers than did the alpha3-peptide. The stability of the r3-peptide helix decreased when the ionic strength of the buffer was increased and when the pH of the buffer was adjusted to 2 or 12. These results suggest that the r3-peptide underwent a "magnet-like" oligomerization and that an increase in the charge-distribution inequality may be the driving force for the formation of fibrous structures.

Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide

To determine if occupancy of interfacial pockets in oligomeric proteins by volatile anesthetic molecules can allosterically regulate oligomerization equilibria, variants of a three-helix bundle peptide able to form higher oligomers were studied with analytical ultracentrifugation, hydrogen exchange and modeling. Halothane shifted the oligomerization equilibria towards the oligomer only in a mutation predicted to create sufficient volume in the hexameric pocket. Other mutations at this residue, predicted to create a too small or too polar pocket, were unaffected by halothane. Inhaled anesthetic modulation of oligomerization interactions is a novel and potentially generalizable biophysical basis for some anesthetic actions.

Metal-assembled modular proteins: toward functional protein design

Metal-assembled parallel helix-bundle proteins have been used to investigate electron transfer through alpha-helical structures. Fermi Golden Rule distance dependence of electron transfer rates was established in a family of designed metalloproteins, and the contribution of intrahelical hydrogen bonding to the matrix tunneling element was explored. The first steps toward the design of functional proteins using dynamic combinatorial assembly of alpha-helical structural elements are described.

Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution

We test molecular level hypotheses for the high thermal stability of alpha-helical conformations of alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid peptide with explicit treatment of water. To assess the contribution of large side chains to alpha-helix stability through backbone desolvation and salt-bridge formation, we simulate the alanine-rich peptide, Ac-YAEAAKAAEAAKAAEAAKAF-Nme, referred to as the EK peptide, that has three pairs of "i, i + 3" glutamic acid(-) and lysine(+) substitutions. Efficient configurational sampling of the EK peptide over a wide temperature range enabled by the replica exchange molecular dynamics technique allows characterization of the stability of alpha-helix with respect to heat-induced unfolding. We find that near ambient temperatures, the EK peptide predominately samples alpha-helical configurations with 80% fractional helicity at 300 K. The helix melts over a broad range of temperatures with melting temperature, T(m), equal to 350 K, that is significantly higher than the T(m) of a 21-residue polyalanine peptide, A(21). Salt-bridges between oppositely charged Glu(-) and Lys(+) side chains can, in principle, provide thermal stability to alpha-helical conformers. For the specific EK peptide sequence, we observe infrequent formation of Glu-Lys salt-bridges (with approximately 10-20% probability) and therefore we conclude that salt-bridge formation does not contribute significantly to the EK peptide's helical stability. However, lysine side chains are found to shield specific "i, i + 4" backbone hydrogen bonds from water, indicating that large side-chain substituents can play an important role in stabilizing alpha-helical configurations of short peptides in aqueous solution through mediation of water access to backbone hydrogen bonds. These observations have implications on molecular engineering of peptides and biomolecules in the design of their thermostable variants where the shielding mechanism can act in concert with other factors such as salt-bridge formation, thereby increasing thermal stability considerably.