The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1–5. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder–target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein–protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.

Although de novo protein design is an important endeavor with implications for understanding protein folding, until now, structures have been determined for only a few 25-to 30-residue designed miniproteins. Here, the NMR solution structure of a complex 73-residue three-helix bundle protein, ␣ 3 D, is reported. The structure of ␣ 3 D was not based on any natural protein, and yet it shows thermodynamic and spectroscopic properties typical of native proteins. A variety of features contribute to its unique structure, including electrostatics, the packing of a diverse set of hydrophobic side chains, and a loop that incorporates common capping motifs. Thus, it is now possible to design a complex protein with a well defined and predictable three-dimensional structure.

We examined the hydration of amides of ␣ 3 D, a simple, designed three-helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the helical axis to interact with solvent water, resulting in a lengthening of the hydrogen bonds on this face of the helix. Water molecules are bonded to these carbonyl groups with partial occupancy (∼ 50%-70%), and their interaction geometries show a large variation in their hydrogen bond lengths and angles on the nsec time scale. This heterogeneity is reflected in the carbonyl stretching vibration (amide IЈ band) of a group of surface Ala residues. The surface-exposed amides are broad, and shift to lower frequency (reflecting strengthening of the hydrogen bonds) as the temperature is decreased. By contrast, the amide IЈ bands of the buried 13 C-labeled Leu residues are significantly sharper and their frequencies are consistent with the formation of strong hydrogen bonds, independent of temperature. The rates of hydrogen-deuterium exchange and the proton NMR chemical shifts of the helical amide groups also depend on environment. The partial occupancy of the hydration sites on the surface of helices suggests that the interaction is relatively weak, on the order of thermal energy at room temperature. One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4-7 residues Nterminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 3 10 /␣/-helical conformation.

Human soluble interleukin-7 receptor (sIL7R)α circulates in high molar excess compared with IL-7, but its biology remains unclear. We demonstrate that sIL7Rα has moderate affinity for IL-7 but does not bind thymic stromal lymphopoietin. Functionally, sIL7Rα competes with cell-associated IL-7 receptor to diminish excessive IL-7 consumption and, thus, enhances the bioactivity of IL-7 when the cytokine is limited, as it is presumed to be in vivo. IL-7 signaling in the presence of sIL7Rα also diminishes expression of CD95 and suppressor of cytokine signaling 1, both regulatory molecules. Murine models confirm diminished consumption of IL-7 in the presence of sIL7Rα and also demonstrate a potentiating effect of sIL7Rα on IL-7-mediated homeostatic expansion and experimental autoimmune encephalomyelitis exacerbation. In multiple sclerosis and several other autoimmune diseases, IL7R genotype influences susceptibility. We measured increased sIL7Rα levels, as well as increased IL-7 levels, in multiple sclerosis patients with the predisposing IL7R genotype, consistent with diminished IL-7 consumption in vivo. This work demonstrates that sIL7Rα potentiates IL-7 bioactivity and provides a basis to explain the increased risk of autoimmunity observed in individuals with genotype-induced elevations of sIL7Rα.immunology | soluble receptors | tolerance

Summary IL-7 and IL-7Rα bind the γc receptor forming a complex crucial to several signaling cascades leading to the development and homeostasis of T and B cells. We report the IL-7Rα ectodomain uses glycosylation to modulate its binding constants to IL-7, unlike the other receptors in the γc family. IL-7 binds glycosylated IL-7Rα 300-fold more tightly than unglycosylated IL-7Rα, and the enhanced affinity is attributed primarily to an accelerated on-rate. Structural comparison of IL-7 in complex to both forms of the IL-7Rα reveals that glycosylation does not participate directly in the binding interface. The SCID mutations of the IL-7Rα locate outside the binding interface with IL-7 suggesting that the expressed mutations cause protein folding defects in IL-7Rα. The IL-7/IL-7Rα structures provide the first view into the molecular recognition events of the IL-7 signaling cascade and provide sites to target for designing new therapeutics to treat IL-7 related diseases.

SUMMARY The common γ-chain (γc) plays a central role in signaling by IL-2 and other γc–dependent cytokines. Here we report that activated T cells produce an alternatively spliced form of γc mRNA that results in protein expression and secretion of the γc extracellular domain. The soluble form of γc (sγc) is present in serum and directly binds to IL-2Rβ and IL-7Rα proteins on T cells to inhibit cytokine signaling and promote inflammation. Sγc suppressed IL-7 signaling to impair naïve T cell survival during homeostasis and exacerbated Th17-cell-mediated inflammation by inhibiting IL-2 signaling upon T cell activation. Reciprocally, the severity of Th17-cell-mediated inflammatory diseases was markedly diminished in mice lacking sγc. Thus, sγc expression is a naturally occurring immunomodulator that regulates γc cytokine signaling and controls T cell activation and differentiation.

There is significant current interest in identifying new combination therapies that synergize to treat disease, and it is becoming increasingly clear that the temporal resolution of their administration greatly impacts efficacy. To facilitate effective delivery, we developed a multicompartment hydrogel material composed of spherical vesicles interlaced within a self-assembled peptide-based network of physically crosslinked fibrils that allows time-resolved independent co-delivery of small molecules. Herein, we demonstrate that this material architecture effectively delivers the EGFR kinase inhibitor erlotinib (ERL) and doxorubicin (DOX, DNA intercalator) in an ERL→DOX sequential manner to synergistically kill glioblastoma, the most aggressive form of brain cancer.

We report here an unliganded receptor structure in the common gamma-chain (γ c ) family of receptors and cytokines. The crystal structure of the unliganded form of the interleukin-7 alpha receptor (IL-7Rα) extracellular domain (ECD) at 2.15 Å resolution reveals a homodimer forming an "X" geometry looking down onto the cell surface with the C termini of the two chains separated by 110 Å and the dimer interface comprising residues critical for IL-7 binding. Further biophysical studies indicate a weak association of the IL-7Rα ECDs but a stronger association between the γ c /IL-7Rα ECDs, similar to previous studies of the full-length receptors on CD4 + T cells. Based on these and previous results, we propose a molecular mechanism detailing the progression from the inactive IL-7Rα homodimer and IL-7Rα-γ c heterodimer to the active IL-7-IL-7Rα-γ c ternary complex whereby the two receptors undergo at least a 90°rotation away from the cell surface, moving the C termini of IL-7Rα and γ c from a distance of 110 Å to less than 30 Å at the cell surface. This molecular mechanism can be used to explain recently discovered IL-7-and γ c -independent gain-of-function mutations in IL-7Rα from B-and Tcell acute lymphoblastic leukemia patients. The mechanism may also be applicable to other γ c receptors that form inactive homodimers and heterodimers independent of their cytokines.X-ray crystallography | biophysics | homodimerization | cancer mutations