Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy

Software to predict the change in protein stability upon point mutation is a valuable tool for a number of biotechnological and scientific problems. To facilitate the development of such software and provide easy access to the available experimental data, the ProTherm database was created. Biases in the methods and types of information collected has led to disparity in the types of mutations for which experimental data is available. For example, mutations to alanine are hugely overrepresented whereas those involving charged residues, especially from one charged residue to another, are underrepresented. ProTherm subsets created as benchmark sets that do not account for this often underrepresent tense certain mutational types. This issue introduces systematic biases into previously published protocols' ability to accurately predict the change in folding energy on these classes of mutations. To resolve this issue, we have generated a new benchmark set with these problems corrected. We have then used the benchmark set to test a number of improvements to the point mutation energetics tools in the Rosetta software suite.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core

VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4_BS) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1–3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.

Automatically Fixing Errors in Glycoprotein Structures with Rosetta

Recent advances in single-particle cryo-electron microscopy (cryoEM) have resulted in determination of an increasing number of protein structures with resolved glycans. However, existing protocols for the refinement of glycoproteins at low resolution have failed to keep up with these advances. As a result, numerous deposited structures contain glycan stereochemical errors. Here, we describe a Rosetta-based approach for both cryoEM and X-ray crystallography refinement of glycoproteins that is capable of correcting conformational and configurational errors in carbohydrates. Building upon a previous Rosetta framework, we introduced additional features and score terms enabling automatic detection, setup, and refinement of glycan-containing structures. We benchmarked this approach using 12 crystal structures and showed that glycan geometries can be automatically improved while maintaining good fit to the crystallographic data. Finally, we used this method to refine carbohydrates of the human coronavirus NL63 spike glycoprotein and of an HIV envelope glycoprotein, demonstrating its usefulness for cryoEM refinement.

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New method for refinement of carbohydrates with low-resolution electron density

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Improved physical geometry of glycans in protein structures

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Compatible with cryoEM and X-ray crystallography data

Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy

The tremendous pandemic potential of coronaviruses was demonstrated twice in the last 15 years by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor‐binding and membrane fusion functions. Despite their biomedical importance, coronavirus S glycoproteins have proven difficult targets for structural characterization, precluding high‐resolution studies of the biologically relevant trimer. Recent technological developments in single particle cryo‐electron microscopy allowed us to determine the first structure of a coronavirus S glycoprotein trimer which provided a framework to understand the mechanisms of viral entry and suggested potential inhibition strategies for this family of viruses. Here, we describe the key factors that enabled this breakthrough.

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions. S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a mouse coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins, implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains.

Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling

Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties, being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here, we present an atomic model of the P pilus generated from a 3.8 Å resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod’s remarkable mechanical properties and illuminates its role in pilus secretion.

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The atomic structure of a chaperone-usher pilus rod was solved by cryo-EM

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Each subunit makes contact with five preceding and five succeeding subunits

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Mutations at subunit-subunit interfaces affect rod formation, not polymerization

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The structure elucidates the molecular basis for rod uncoiling

New implant designs for fracture fixation in osteoporotic bone

Screws are one of the limiting factors for fixation of implants, particularly in poor bone quality. A class of new implants with an implant-bone-interface optimized regarding load transition by increasing the peripheral area might improve the anchorage of implants in osteoporotic bone. However, the shape of these implants requires new technologies for insertion. The goal of the work presented here was to analyze the relevant parameters regarding implant geometry and to demonstrate the effect of new procedures for their insertion. The investigation was divided into three parts: 1) implant design optimisation, 2) efficiency of cortical bone ablation, and 3) implant insertion technology. Finite element analysis (FEA) was performed to investigate the influence of the number of lobes, the radius of the outer curvature and additional milling to remove any sharp changes of section around the lobe. Opening of the cortical bone with an Er:YAG laser was studied using calf cortex from 2 to 7 mm thickness. The effect of a) pulse energy and pulse duration, b) cortical thickness, c) wet or dry boundary conditions on volume and geometry of ablated bone, time required to penetrate the cortical bone and local bone tissue damage was quantified. Pneumatic and ultrasound based insertion were compared in the third experiment. The cortical bone was prepared in the following ways: a) no opening, b) predrilling of three holes (1 mm diameter each) and c) exact pre-cutting of the whole contour. Increasing the radius of the outer curvature from 2 to 5 mm reduces the peak stresses during loading in all planes in the implant as well as in the adjacent cortical bone by about 30-40%. An increase in the number of lobes from two to three decreases the mean peak stress by about 46% (alpha < 0.001) and the range between the minimal and maximal peak stresses for different loading directions by about 83%. Penetration of cortical bone with an Er:YAG laser was possible up to a cortical thickness of 6 mm with fewer than 100 pulses. The ablation rate per pulse increased more with increasing duration than with increasing energy. Signs of bone damage such as melting were only visible when high pulse energies and durations were used. Insertion of the prototype was possible with all devices, but only when the whole contour was cut out of the cortical bone. However, the use of the ultrasound vibrator led to heating up of the tissue fluid and subsequently to water evaporation and tissue damage. Insertion of the prototype was possible with both pneumatic vibrators, but only when the whole contour was cut out of the cortical bone. New implant designs may lead to reduced stress peaks in the surrounding bone and might be inserted with the help of new insertion technologies, namely laser cutting of cortical bone and pneumatic vibration. Further studies are required to optimize these technologies prior to clinical use.