Computational design of the affinity and specificity of a therapeutic T cell receptor

T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities

Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering

We describe a framework for designing the sequences of multiple nucleic acid strands intended to hybridize in solution via a prescribed reaction pathway. Sequence design is formulated as a multistate optimization problem using a set of target test tubes to represent reactant, intermediate, and product states of the system, as well as to model crosstalk between components. Each target test tube contains a set of desired “on-target” complexes, each with a target secondary structure and target concentration, and a set of undesired “off-target” complexes, each with vanishing target concentration. Optimization of the equilibrium ensemble properties of the target test tubes implements both a positive design paradigm, explicitly designing for on-pathway elementary steps, and a negative design paradigm, explicitly designing against off-pathway crosstalk. Sequence design is performed subject to diverse user-specified sequence constraints including composition constraints, complementarity constraints, pattern prevention constraints, and biological constraints. Constrained multistate sequence design facilitates nucleic acid reaction pathway engineering for diverse applications in molecular programming and synthetic biology. Design jobs can be run online via the NUPACK web application

Microwave Components with MEMS Switches

RF MEMS switches with metal-metal contacts are being developed for microwave applications where broadband, high linearity performance is required. These switches provide less than 0.2 dB insertion loss through 40 GHz. This paper describes the integration of these switches into selected microwave components such as reconfigurable antenna elements, tunable filters, switched delay lines, and SPDT switches. Microwave and millimeter wave measured results from these circuits are presented

A Theoretical Investigation of the One– and Two–photon Properties of Porphyrins

The one‐ and two‐photon properties of free base porphin, free base porphin dianion, and the 2,4‐substituted diformyl and divinyl analogs of these molecules are studied using a semiempirical SCF‐MO formalism (CNDO‐π‐SCF‐MO‐PSDCI) including extensive single and double configuration interaction. Strongly two‐photon allowed states are predicted to lie in the Soret region as well as in the region between the Soret and visible bands. A number of the two‐photon allowed states in the Soret region are predicted to have two‐photon absorptivities exceeding 100×10−50 cm4 s molecule−1 photon−1. The calculations indicate that the visible (Q) states are well characterized by the four orbital model, whereas the Soret (B) states contain significant contributions from configurations comprised of other orbitals. The inclusion of extensive double configuration interaction significantly reduces the Soret‐visible (B–Q) splitting, increases the Qx–Qy splitting, and yields calculated oscillator strengths for the Qbands in better agreement with experiment than values calculated using single CI alone. The effects of conjugation into the porphyrin macrocycle are predicted to be more significant than inductive effects on macrocycle π orbitals due to substituent polarity. The 〈Qx‖r‖S0〉 and 〈Qy‖r‖S0〉 transition moment vectors are predicted to lie approximately through adjacent pyrrole rings in 2‐ and 4‐monoformyl free base porphin dianions and approximately through adjacent methine bridges in 2,4‐diformyl free base porphin dianion

How structural adaptability exists alongside HLA-A2 bias in the human alphabeta TCR repertoire

How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining alphabeta TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged hot-spot region that is almost exclusive to the alpha1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Valpha and Vbeta genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs

Selective Nucleic Acid Capture with Shielded Covalent Probes

Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2–3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1–2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo)

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

We present an updated and integrated version of our widely used protein–protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein–protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody–antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top 10 docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r = 0.52 overall and r = 0.72 for the rigid complexes.Peer ReviewedPostprint (author's final draft

Structure and Thermochemistry of Perrhenate Sodalite and Mixed Guest Perrhenate/Pertechnetate Sodalite.

Treatment and immobilization of technetium-99 (99Tc) contained in reprocessed nuclear waste and present in contaminated subsurface systems represents a major environmental challenge. One potential approach to managing this highly mobile and long-lived radionuclide is immobilization into micro- and meso-porous crystalline solids, specifically sodalite. We synthesized and characterized the structure of perrhenate sodalite, Na8[AlSiO4]6(ReO4)2, and the structure of a mixed guest perrhenate/pertechnetate sodalite, Na8[AlSiO4]6(ReO4)2-x(TcO4)x. Perrhenate was used as a chemical analogue for pertechnetate. Bulk analyses of each solid confirm a cubic sodalite-type structure (P4̅3n, No. 218 space group) with rhenium and technetium in the 7+ oxidation state. High-resolution nanometer scale characterization measurements provide first-of-a-kind evidence that the ReO4- anions are distributed in a periodic array in the sample, nanoscale clustering is not observed, and the ReO4- anion occupies the center of the sodalite β-cage in Na8[AlSiO4]6(ReO4)2. We also demonstrate, for the first time, that the TcO4- anion can be incorporated into the sodalite structure. Lastly, thermochemistry measurements for the perrhenate sodalite were used to estimate the thermochemistry of pertechnetate sodalite based on a relationship between ionic potential and the enthalpy and Gibbs free energy of formation for previously measured oxyanion-bearing feldspathoid phases. The results collected in this study suggest that micro- and mesoporous crystalline solids maybe viable candidates for the treatment and immobilization of 99Tc present in reprocessed nuclear waste streams and contaminated subsurface environments

Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

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