Computational design of non-porous pH-responsive antibody nanoparticles.

Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and is important for targeted delivery of biologics. Here we describe the design of octahedral non-porous nanoparticles with a targeting antibody on the two-fold symmetry axis, a designed trimer programmed to disassemble below a tunable pH transition point on the three-fold axis, and a designed tetramer on the four-fold symmetry axis. Designed non-covalent interfaces guide cooperative nanoparticle assembly from independently purified components, and a cryo-EM density map closely matches the computational design model. The designed nanoparticles can package protein and nucleic acid payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between 5.9 and 6.7. The ability to incorporate almost any antibody into a non-porous pH-dependent nanoparticle opens up new routes to antibody-directed targeted delivery.

Computational design of non-porous, pH-responsive antibody nanoparticles.

Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and important for targeted delivery of biologics. We describe the design of octahedral non-porous nanoparticles with the three symmetry axes (four-fold, three-fold, and two-fold) occupied by three distinct protein homooligomers: a de novo designed tetramer, an antibody of interest, and a designed trimer programmed to disassemble below a tunable pH transition point. The nanoparticles assemble cooperatively from independently purified components, and a cryo-EM density map reveals that the structure is very close to the computational design model. The designed nanoparticles can package a variety of molecular payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between to 5.9-6.7. To our knowledge, these are the first designed nanoparticles with more than two structural components and with finely tunable environmental sensitivity, and they provide new routes to antibody-directed targeted delivery.

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus.

Respiratory syncytial virus (RSV) is a worldwide public health concern for which no vaccine is available. Elucidation of the prefusion structure of the RSV F glycoprotein and its identification as the main target of neutralizing antibodies have provided new opportunities for development of an effective vaccine. Here, we describe the structure-based design of a self-assembling protein nanoparticle presenting a prefusion-stabilized variant of the F glycoprotein trimer (DS-Cav1) in a repetitive array on the nanoparticle exterior. The two-component nature of the nanoparticle scaffold enabled the production of highly ordered, monodisperse immunogens that display DS-Cav1 at controllable density. In mice and nonhuman primates, the full-valency nanoparticle immunogen displaying 20 DS-Cav1 trimers induced neutralizing antibody responses ∼10-fold higher than trimeric DS-Cav1. These results motivate continued development of this promising nanoparticle RSV vaccine candidate and establish computationally designed two-component nanoparticles as a robust and customizable platform for structure-based vaccine design.

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as ROSETTA3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.

Structure prediction for CASP8 with all-atom refinement using Rosetta.

We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.

RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.

We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.

Ranking predicted protein structures with support vector regression.

Protein structure prediction is an important problem of both intellectual and practical interest. Most protein structure prediction approaches generate multiple candidate models first, and then use a scoring function to select the best model among these candidates. In this work, we develop a scoring function using support vector regression (SVR). Both consensus-based features and features from individual structures are extracted from a training data set containing native protein structures and predicted structural models submitted to CASP5 and CASP6. The SVR learns a scoring function that is a linear combination of these features. We test this scoring function on two data sets. First, when used to rank server models submitted to CASP7, the SVR score selects predictions that are comparable to the best performing server in CASP7, Zhang-Server, and significantly better than all the other servers. Even if the SVR score is not allowed to select Zhang-Server models, the SVR score still selects predictions that are significantly better than all the other servers. In addition, the SVR is able to select significantly better models and yield significantly better Pearson correlation coefficients than the two best Quality Assessment groups in CASP7, QA556 (LEE), and QA634 (Pcons). Second, this work aims to improve the ability of the Robetta server to select best models, and hence we evaluate the performance of the SVR score on ranking the Robetta server template-based models for the CASP7 targets. The SVR selects significantly better models than the Robetta K*Sync consensus alignment score.

A learned comparative expression measure for affymetrix genechip DNA microarrays.

Perhaps the most common question that a microarray study can ask is, "Between two given biological conditions, which genes exhibit changed expression levels?" Existing methods for answering this question either generate a comparative measure based upon a static model, or take an indirect approach, first estimating absolute expression levels and then comparing the estimated levels to one another. We present a method for detecting changes in gene expression between two samples based on data from Affymetrix GeneChips. Using a library of over 200,000 known cases of differential expression, we create a learned comparative expression measure (LCEM) based on classification of probe-level data patterns as changed or unchanged. LCEM uses perfect match probe data only; mismatch probe values did not prove to be useful in this context. LCEM is particularly powerful in the case of small microarry studies, in which a regression-based method such as RMA cannot generalize, and in detecting small expression changes. At the levels of selectivity that are typical in microarray analysis, the LCEM shows a lower false discovery rate than either MAS5 or RMA trained from a single chip. When many chips are available to RMA, LCEM performs better on two out of the three data sets, and nearly as well on the third. Performance of the MAS5 log ratio statistic was notably bad on all datasets.