Atomistic study of CoCrCuFeNi high entropy alloy nanoparticles: Role of chemical complexity.

High entropy alloy nanoparticles are envisaged as one of the most interesting materials compared to monoatomic materials due to their modulated properties in terms of their convenient surface-to-volume ratio. However, studies are still missing to unveil how composition or nanoparticle size can influence nanoparticle morphology. Based on molecular dynamics simulations, we perform a structural characterization as a function of nanoparticle size and the chemical composition of high entropy alloy nanoparticles subject to multiple annealing cycles. After the multiple thermal loads, we observe a substantial migration of copper atoms towards the np surface, consistent with the experimental results of Cu-based high entropy alloys. The resulting high entropy alloy nanoparticle behaves as a core-shell nanostructure with a rich fcc phase on the surface (50% of Cu) and 5% fcc phase in the nanoparticle core. Inspecting the nanoparticle surface, it is observed that high entropy alloy nanoparticles have a lack of surface facets, leading to a more spherical shape, quite different from mono-metallic nanoparticles with a high number of facets. Performing an average atoms simulation, it showed that nanoparticles are prone to form 111 surface facets independent of the nanoparticle size, suggesting that for high entropy alloy nanoparticles, the chemical complexity avoids the formation of surface facets. The latter can be explained in terms of the lattice distortion inducing tensile/compressive stress that drives the surface reconstruction. All in all our results match extremely well with experimental evidence of FeNiCrCoCu nanocrystalline materials, explaining the Cu segregation in terms of surface energy and mixing enthalpy criteria. We believe that our results provide a detailed characterization of high entropy nanoparticles focusing on how chemical complexity induces morphological changes compared to mono-crystalline nanoparticles. Besides, our findings are valuable for experimental works aimed at designing the shape and composition of multicomponent nanoparticles.

Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions.

Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.

Probing the Mechanical Properties of Porous Nanoshells by Nanoindentation.

In this contribution, we present a study of the mechanical properties of porous nanoshells measured with a nanoindentation technique. Porous nanoshells with hollow designs can present attractive mechanical properties, as observed in hollow nanoshells, but coupled with the unique mechanical behavior of porous materials. Porous nanoshells display mechanical properties that are dependent on shell porosity. Our results show that, under smaller porosity values, deformation is closely related to the one observed for polycrystalline and single-crystalline nanoshells involving dislocation activity. When porosity in the nanoparticle is increased, plastic deformation was mediated by grain boundary sliding instead of dislocation activity. Additionally, porosity suppresses dislocation activity and decreases nanoparticle strength, but allows for significant strain hardening under strains as high as 0.4. On the other hand, Young's modulus decreases with the increase in nanoshell porosity, in agreement with the established theories of porous materials. However, we found no quantitative agreement between conventional models applied to obtain the Young's modulus of porous materials.

Thermal Sensitivity on Eccentric Gold Hollow Nanoparticles: A Perspective from Atomistic Simulations.

Eccentricity is a common feature consequence of several synthesis protocols of hollow nanoshells. Despite the crescent interest in these nanoparticles, it is still unclear how an irregular layer on the nanoparticle impacts the macroscopic properties. Here, we study the thermal stability of eccentric hollow nanoparticles (hNPs) for different sizes and eccentricity values by means of classical molecular dynamics simulations. Our results reveal that eccentricity displays a significant role in the thermal stability of hNPs. We attribute this behavior to the irregular shell contour, which collapses due to the thermal-activated diffusive process from the nanoparticle shell's most thin region. The mechanism is driven at low temperature by the nucleation of stacking faults until the amorphization for larger temperature values. Besides, for some particular eccentric hNPs, the shell suffers a surface reconstruction process, transforming the eccentric hNP into a concentric hNP. We believe that our study on thermal effects in eccentric hNPs has relevance because of their outstanding applications for plasmonic and sensing.

Thermal Stability of Hollow Porous Gold Nanoparticles: A Molecular Dynamics Study.

Hollow nanoparticle structures play a major role in nanotechnology and nanoscience since their surface to volume ratio is significantly larger than that of filled ones. While porous hollow nanoparticles offer a significant improvement of the available surface area, there is a lack of theoretical understanding, and scarce experimental information, on how the porosity controls or dominates the stability. Here we use classical molecular dynamics simulations to shed light on the particular characteristics and properties of gold porous hollow nanoparticles and how they differ from the nonporous ones. Adopting gold as a prototype, we show how, as the temperature increases, the porosity introduces surface stress and minor transitions that lead to various scenarios, from partial shrinkage for small filling factors to abrupt compression and the loss of spherical shape for large filling. Our work provides new insights into the stability limits of porous hollow nanoparticles, with important implications for the design and practical use of these enhanced geometries.

Toward Biological Pacing by Cellular Delivery of Hcn2/SkM1.

Electronic pacemakers still face major shortcomings that are largely intrinsic to their hardware-based design. Radical improvements can potentially be generated by gene or cell therapy-based biological pacemakers. Our previous work identified adenoviral gene transfer of Hcn2 and SkM1, encoding a "funny current" and skeletal fast sodium current, respectively, as a potent combination to induce short-term biological pacing in dogs with atrioventricular block. To achieve long-term biological pacemaker activity, alternative delivery platforms need to be explored and optimized. The aim of the present study was therefore to investigate the functional delivery of Hcn2/SkM1 via human cardiomyocyte progenitor cells (CPCs). Nucleofection of Hcn2 and SkM1 in CPCs was optimized and gene transfer was determined for Hcn2 and SkM1 in vitro. The modified CPCs were analyzed using patch-clamp for validation and characterization of functional transgene expression. In addition, biophysical properties of Hcn2 and SkM1 were further investigated in lentivirally transduced CPCs by patch-clamp analysis. To compare both modification methods in vivo, CPCs were nucleofected or lentivirally transduced with GFP and injected in the left ventricle of male NOD-SCID mice. After 1 week, hearts were collected and analyzed for GFP expression and cell engraftment. Subsequent functional studies were carried out by computational modeling. Both nucleofection and lentiviral transduction of CPCs resulted in functional gene transfer of Hcn2 and SkM1 channels. However, lentiviral transduction was more efficient than nucleofection-mediated gene transfer and the virally transduced cells survived better in vivo. These data support future use of lentiviral transduction over nucleofection, concerning CPC-based cardiac gene delivery. Detailed patch-clamp studies revealed Hcn2 and Skm1 current kinetics within the range of previously reported values of other cell systems. Finally, computational modeling indicated that CPC-mediated delivery of Hcn2/SkM1 can generate stable pacemaker function in human ventricular myocytes. These modeling studies further illustrated that SkM1 plays an essential role in the final stage of diastolic depolarization, thereby enhancing biological pacemaker functioning delivered by Hcn2. Altogether these studies support further development of CPC-mediated delivery of Hcn2/SkM1 and functional testing in bradycardia models.

Modeling interacting city traffic with finite acceleration and braking capacities.

Understanding the fundamental interactions in the complex behavior of one car moving in a sequence of traffic lights necessarily implies the inclusion of finite braking and accelerating capabilities. This characteristic is usually not considered in the standard cellular automaton models, where car interactions are the main concern. Therefore, here we develop a model which includes interactions and finite braking and accelerating capabilities, filling the gap between a standard cellular automaton model that considers car interactions but infinite braking and accelerating capabilities and the continuous one car model that includes finite braking and accelerating capabilities but does not consider, as the name indicates, car interactions. The proposed new model bridge these two seemingly different approaches in an effort to investigate how the traffic jams are produced. We found that, in the appropriate limits, we can reproduce the complex behavior of the one car continuous model and the dynamics close to the resonance induced by the interacting cars, forced by the traffic lights. In the processes of introducing car interactions, we observe how the average velocity decreases to finally obtain traffic jams, which are an emergent state in which the traffic lights control the generation of pulses of cars but do not control its average speed. This model is expected to improve our understanding of the complexity that appears in city traffic situations, as the finite braking and accelerating capabilities are necessary to describe the vehicle dynamics, the control strategy of traffic light synchronization, the motion of buses in segregated lights, and the whole urban design.

Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence.

Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinants we generated a SOSIP trimer based on a consensus sequence of all HIV-1 group M isolates (ConM). The ConM trimer displays the epitopes of most known bNAbs and several germline bNAb precursors. The crystal structure of the ConM trimer at 3.9 Å resolution resembles that of the native Env trimer and its antigenic surface displays few rare residues. The ConM trimer elicits strong NAb responses against the autologous virus in rabbits and macaques that are significantly enhanced when it is presented on ferritin nanoparticles. The dominant NAb specificity is directed against an epitope at or close to the trimer apex. Immunogens based on consensus sequences might have utility in engineering vaccines against HIV-1 and other viruses.

Stabilization of the V2 loop improves the presentation of V2 loop-associated broadly neutralizing antibody epitopes on HIV-1 envelope trimers.

A successful HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs) that target the envelope glycoprotein (Env) spike on the virus. Native-like recombinant Env trimers of the SOSIP design now serve as a platform for achieving this challenging goal. However, SOSIP trimers usually do not bind efficiently to the inferred germline precursors of bNAbs (gl-bNAbs). We hypothesized that the inherent flexibilities of the V1 and V2 variable loops in the Env trimer contribute to the poor recognition of gl-bNAb epitopes at the trimer apex that extensively involve V2 residues. To reduce local V2 flexibility and improve the binding of V2-dependent bNAbs and gl-bNAbs, we designed BG505 SOSIP.664 trimer variants containing newly created disulfide bonds intended to stabilize the V2 loop in an optimally antigenic configuration. The first variant, I184C/E190C, contained a new disulfide bond within the V2 loop, whereas the second variant, E153C/R178C, had a new disulfide bond that cross-linked V2 and V1. The resulting engineered native-like trimer variants were both more reactive with and were neutralized by V2 bNAbs and gl-bNAbs, a finding that may be valuable in the design of germline targeting and boosting trimer immunogens to create an antigenic conformation optimal for HIV vaccine development.

Developability Assessment of Physicochemical Properties and Stability Profiles of HIV-1 BG505 SOSIP.664 and BG505 SOSIP.v4.1-GT1.1 gp140 Envelope Glycoprotein Trimers as Candidate Vaccine Antigens.

The induction of broadly neutralizing antibodies (bNAbs) is a major goal in the development of an effective vaccine against HIV-1. A soluble, trimeric, germline (gI) bNAb-targeting variant of the HIV-1 envelope glycoprotein (termed BG505 SOSIP.v4.1-GT1.1 gp140, abbreviated to GT1.1) has recently been developed. Here, we have compared this new immunogen with the parental trimer from which it was derived, BG505 SOSIP.664 gp140. We used a comprehensive suite of biochemical and biophysical methods to determine physicochemical similarities and differences between the 2 trimers, and thereby assessed whether additional formulation development efforts were needed for the GT1.1 vaccine candidate. The overall higher order structure and oligomeric states of the 2 vaccine antigens were quite similar, as were their thermal, chemical, and colloidal stability profiles, as evaluated during accelerated stability studies. Overall, we conclude that the primary sequence changes made to create the gl bNAb-targeting GT1.1 trimer did not detrimentally affect its physicochemical properties or stability profiles from a pharmaceutical perspective. This developability assessment of the BG505 GT1.1 vaccine antigen supports using the formulation and storage conditions previously identified for the parental SOSIP.664 trimer and enables the development of GT1.1 for phase I clinical studies.

Inference of the HIV-1 VRC01 Antibody Lineage Unmutated Common Ancestor Reveals Alternative Pathways to Overcome a Key Glycan Barrier.

Elicitation of VRC01-class broadly neutralizing antibodies (bnAbs) is an appealing approach for a preventative HIV-1 vaccine. Despite extensive investigations, strategies to induce VRC01-class bnAbs and overcome the barrier posed by the envelope N276 glycan have not been successful. Here, we inferred a high-probability unmutated common ancestor (UCA) of the VRC01 lineage and reconstructed the stages of lineage maturation. Env immunogens designed on reverted VRC01-class bnAbs bound to VRC01 UCA with affinity sufficient to activate naive B cells. Early mutations defined maturation pathways toward limited or broad neutralization, suggesting that focusing the immune response is likely required to steer B cell maturation toward the development of neutralization breadth. Finally, VRC01 lineage bnAbs with long CDR H3s overcame the HIV-1 N276 glycan barrier without shortening their CDR L1, revealing a solution for broad neutralization in which the heavy chain, not CDR L1, is the determinant to accommodate the N276 glycan.

Site-Specific Glycosylation of Virion-Derived HIV-1 Env Is Mimicked by a Soluble Trimeric Immunogen.

Many broadly neutralizing antibodies (bnAbs) against HIV-1 recognize and/or penetrate the glycan shield on native, virion-associated envelope glycoprotein (Env) spikes. The same bnAbs also bind to recombinant, soluble trimeric immunogens based on the SOSIP design. While SOSIP trimers are close structural and antigenic mimics of virion Env, the extent to which their glycan structures resemble ones on infectious viruses is undefined. Here, we compare the overall glycosylation of gp120 and gp41 subunits from BG505 (clade A) virions produced in a lymphoid cell line with those from recombinant BG505 SOSIP trimers, including CHO-derived clinical grade material. We also performed detailed site-specific analyses of gp120. Glycans relevant to key bnAb epitopes are generally similar on the recombinant SOSIP and virion-derived Env proteins, although the latter do contain hotspots of elevated glycan processing. Knowledge of native versus recombinant Env glycosylation will guide vaccine design and manufacturing programs.

Integrity of Glycosylation Processing of a Glycan-Depleted Trimeric HIV-1 Immunogen Targeting Key B-Cell Lineages.

Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans, while mature bNAbs can evolve to accommodate or bypass these shielding glycans. The design of germline-targeting Env immunogens therefore includes the targeted deletion of specific glycan sites. However, the processing of glycans on Env trimers can be influenced by the density with which they are packed together, a highly relevant point given the essential contributions under-processed glycans make to multiple bNAb epitopes. We sought to determine the impact of the removal of 15 potential N-glycan sites (5 per protomer) from the germline-targeting soluble trimer, BG505 SOSIP.v4.1-GT1, using quantitative, site-specific N-glycan mass spectrometry analysis. We find that, compared with SOSIP.664, there was little overall change in the glycan profile but only subtle increases in the extent of processing at sites immediately adjacent to where glycans had been deleted. We conclude that multiple glycans can be deleted from BG505 SOSIP trimers without perturbing the overall integrity of the glycan shield.

The microanatomic segregation of selection by apoptosis in the germinal center.

B cells undergo rapid cell division and affinity maturation in anatomically distinct sites in lymphoid organs called germinal centers (GCs). Homeostasis is maintained in part by B cell apoptosis. However, the precise contribution of apoptosis to GC biology and selection is not well defined. We developed apoptosis-indicator mice and used them to visualize, purify, and characterize dying GC B cells. Apoptosis is prevalent in the GC, with up to half of all GC B cells dying every 6 hours. Moreover, programmed cell death is differentially regulated in the light zone and the dark zone: Light-zone B cells die by default if they are not positively selected, whereas dark-zone cells die when their antigen receptors are damaged by activation-induced cytidine deaminase.

Design and crystal structure of a native-like HIV-1 envelope trimer that engages multiple broadly neutralizing antibody precursors in vivo.

Induction of broadly neutralizing antibodies (bNAbs) by HIV-1 envelope glycoprotein immunogens would be a major advance toward an effective vaccine. A critical step in this process is the activation of naive B cells expressing germline (gl) antibody precursors that have the potential to evolve into bNAbs. Here, we reengineered the BG505 SOSIP.664 glycoprotein to engage gl precursors of bNAbs that target either the trimer apex or the CD4-binding site. The resulting BG505 SOSIP.v4.1-GT1 trimer binds multiple bNAb gl precursors in vitro. Immunization experiments in knock-in mice expressing gl-VRC01 or gl-PGT121 show that this trimer activates B cells in vivo, resulting in the secretion of specific antibodies into the sera. A crystal structure of the gl-targeting trimer at 3.2-Å resolution in complex with neutralizing antibodies 35O22 and 9H+109L reveals a native-like conformation and the successful incorporation of design features associated with binding of multiple gl-bNAb precursors.

Stabilized HIV-1 envelope glycoprotein trimers for vaccine use.

PURPOSE OF REVIEW: To provide an update on the latest developments in the field of HIV-1 antibody-based soluble envelope glycoprotein (Env) trimer design for vaccine use. RECENT FINDINGS: The development of soluble native-like HIV-1 Env trimer immunogens has moved the field of antibody-based vaccine design forward dramatically over the past few years with refinement of various stabilizing approaches. However, despite this progress, significant challenges remain. Firstly, although trimers are relatively stable in solution, they nevertheless sample different conformational states, some of which may be less relevant to binding and induction of broadly neutralizing antibodies (bNAbs). Secondly, these trimers expose unwanted immunodominant surfaces that may distract the adaptive immune response from recognizing more immunorecessive but conserved neutralization-relevant surfaces on the trimer. The availability of atomic-resolution structural information has allowed guided design of mutations that have further stabilized trimers and allowed reduced exposure of unwanted epitopes. Moreover, chemical cross-linking approaches that do not require structural information have also contributed to trimer stabilization and selection of particular conformational forms. However, current knowledge suggests that strategies additional to trimer stabilization will be required to elicit bNAb, including targeting naïve B cell receptors with specific immunogens, and guiding B cell lineages toward recognizing conserved surfaces on Env with high affinity. SUMMARY: This review will give a perspective on these challenges, and summarize current approaches to overcoming them with the aim of developing immunogens to elicit bNAb responses in humans by active vaccination.

Energetic, Structural, and Vibrational Properties of 4,4'-Methylenediphenyl Diisocyanate with Relevance for Adhesion.

Through a polymerization process, the monomer 4,4'-methylenediphenyl diisocyanate can participate in glueing, whereby strong covalent bonds between the monomer and the substrates that will be glued have to be formed. In the present work, we use density functional theory (DFT) calculations to study a group of properties that are important for the initial steps of this process and for its experimental characterization. We focus on energetic and structural properties of a single monomer of 4,4'-methylenediphenyl diisocyanate as obtained using different theoretical approaches. We demonstrate that the molecule is chiral and that for each chirality, three different structures, differing in the orientations of the isocyanate groups, can be identified. The molecule is soft against certain geometry transformations and can, accordingly, easily take a structure that is optimal for the formation of covalent bonds with a substrate. Infrared spectroscopy may be used in identifying these covalent bonds, and therefore, these spectra were calculated, and we identify the most relevant vibrations in this context. Finally, changes in the properties when the monomer was modified or when it was allowed to interact with other molecules were studied, too.

Binding of inferred germline precursors of broadly neutralizing HIV-1 antibodies to native-like envelope trimers.

HIV-1 envelope glycoproteins (Env) and Env-based immunogens usually do not interact efficiently with the inferred germline precursors of known broadly neutralizing antibodies (bNAbs). This deficiency may be one reason why Env and Env-based immunogens are not efficient at inducing bNAbs. We evaluated the binding of 15 inferred germline precursors of bNAbs directed to different epitope clusters to three soluble native-like SOSIP.664 Env trimers. We found that native-like SOSIP.664 trimers bind to some inferred germline precursors of bNAbs, particularly ones involving the V1/V2 loops at the apex of the trimer. The data imply that native-like SOSIP.664 trimers will be an appropriate platform for structure-guided design improvements intended to create immunogens able to target the germline precursors of bNAbs.

HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers.

A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs.

Targeting B-cell germlines and focusing affinity maturation: the next hurdles in HIV-1-vaccine development?

Vaccines that protect against viral infection usually elicit neutralizing antibodies, but HIV-1 vaccine candidates have failed to induce broad and potent such responses. Broadly active neutralizing antibodies (bNAbs) do, however, slowly emerge in a minority of HIV-1-infected subjects; and passive immunization with bNAbs protects against viral acquisition in animal models of HIV-1 infection. New techniques have made it possible to interrogate human B cells and thereby to isolate highly potent bNAbs to uncharted epitope clusters. Furthermore, recent high-resolution structure determinations of near-native soluble envelope glycoprotein trimers in complex with different bNAbs reveal the molecular basis for neutralization. Such trimer structures may serve as blueprints for vaccine design. Here we discuss how a vaccine might bridge a reactivity gap from germline antibody to bNAb and simulate the intricate stimuli of affinity maturation that sometimes prevail in chronic infection.