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Xu, Kai

Publications and source records attributed to Xu, Kai.

15 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Human CD4-binding site antibody elicited by polyvalent DNA prime-protein boost vaccine neutralizes cross-clade tier-2-HIV strains

The vaccine elicitation of HIV tier-2-neutralization antibodies has been a challenge. Here, we report the isolation and characterization of a CD4-binding site (CD4bs) specific monoclonal antibody, HmAb64, from a human volunteer immunized with a polyvalent DNA prime-protein boost HIV vaccine. HmAb64 is derived from heavy chain variable germline gene IGHV1-18 and light chain germline gene IGKV1-39. It has a third heavy chain complementarity-determining region (CDR H3) of 15 amino acids. On a cross-clade panel of 208 HIV-1 pseudo-virus strains, HmAb64 neutralized 20 (10%), including tier-2 strains from clades B, BC, C, and G. The cryo-EM structure of the antigen-binding fragment of HmAb64 in complex with a CNE40 SOSIP trimer revealed details of its recognition; HmAb64 uses both heavy and light CDR3s to recognize the CD4-binding loop, a critical component of the CD4bs. This study demonstrates that a gp120-based vaccine can elicit antibodies capable of tier 2-HIV neutralization.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site

The HIV-1 fusion peptide (FP) represents a promising vaccine target, but global FP sequence diversity among circulating strains has limited anti-FP antibodies to ~60% neutralization breadth. Here we evolve the FP-targeting antibody VRC34.01 in vitro to enhance FP-neutralization using site saturation mutagenesis and yeast display. Successive rounds of directed evolution by iterative selection of antibodies for binding to resistant HIV-1 strains establish a variant, VRC34.01_mm28, as a best-in-class antibody with 10-fold enhanced potency compared to the template antibody and ~80% breadth on a cross-clade 208-strain neutralization panel. Structural analyses demonstrate that the improved paratope expands the FP binding groove to accommodate diverse FP sequences of different lengths while also recognizing the HIV-1 Env backbone. These data reveal critical antibody features for enhanced neutralization breadth and potency against the FP site of vulnerability and accelerate clinical development of broad HIV-1 FP-targeting vaccines and therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization

The HIV-1 fusion peptide has been identified as a site for elicitation of broadly neutralizing antibodies, with prior studies demonstrating that priming with fusion peptide-based immunogens and boosting with soluble envelope (Env) trimers can elicit cross-clade HIV-1-neutralizing responses. To improve the neutralizing breadth and potency of fusion peptide-directed responses, we evaluated vaccine regimens that incorporated diverse fusion peptide-conjugates and Env trimers with variation in fusion peptide length and sequence.

Virology↗
DOE OSTI2022

Engineering Interlayer Electron–Phonon Coupling in WS 2 /BN Heterostructures

In van der Waals (vdW) heterostructures, the interlayer electron–phonon coupling (EPC) provides one unique channel to nonlocally engineer these elementary particles. However, limited by the stringent occurrence conditions, the efficient engineering of interlayer EPC remains elusive. Here we report a multitier engineering of interlayer EPC in WS2/boron nitride (BN) heterostructures, including isotope enrichments of BN substrates, temperature, and high-pressure tuning. The hyperfine isotope dependence of Raman intensities was unambiguously revealed. In combination with theoretical calculations, we anticipate that WS2/BN supercells could induce Brillouin-zone-folded phonons that contribute to the interlayer coupling, leading to a complex nature of broad Raman peaks. We further demonstrate the significance of a previously unexplored parameter, the interlayer spacing. By varying the temperature and high pressure, we effectively manipulated the strengths of EPC with on/off capabilities, indicating critical thresholds of the layer–layer spacing for activating and strengthening interlayer EPC. Our findings provide new opportunities to engineer vdW heterostructures with controlled interlayer coupling.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

The Ephb2 Receptor Uses Homotypic, Head-to-Tail Interactions within Its Ectodomain as an Autoinhibitory Control Mechanism

The Eph receptor tyrosine kinases and their ephrin ligands direct axon pathfinding and neuronal cell migration, as well as mediate many other cell–cell communication events. Their dysfunctional signaling has been shown to lead to various diseases, including cancer. The Ephs and ephrins both localize to the plasma membrane and, upon cell–cell contact, form extensive signaling assemblies at the contact sites. The Ephs and the ephrins are divided into A and B subclasses based on their sequence conservation and affinities for each other. The molecular details of Eph–ephrin recognition have been previously revealed and it has been documented that ephrin binding induces higher-order Eph assemblies, which are essential for full biological activity, via multiple, distinct Eph–Eph interfaces. One Eph–Eph interface type is characterized by a homotypic, head-to-tail interaction between the ligand-binding and the fibronectin domains of two adjacent Eph molecules. While the previous Eph ectodomain structural studies were focused on A class receptors, we now report the crystal structure of the full ectodomain of EphB2, revealing distinct and unique head-to-tail receptor–receptor interactions. The EphB2 structure and structure-based mutagenesis document that EphB2 uses the head-to-tail interactions as a novel autoinhibitory control mechanism for regulating downstream signaling and that these interactions can be modulated by posttranslational modifications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs

RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Higher-rank tensor field theory of non-abelian fracton and embeddon

We formulate a new class of tensor gauge field theories in any dimension that is a hybrid class between symmetric higher-rank tensor gauge theory (i.e., higher-spin gauge theory) and anti-symmetric tensor topological field theory. Our theory describes a mixed unitary phase interplaying between gapless and gapped topological order phases (which can live with or without Euclidean, Poincaré, or anisotropic symmetry, at least in ultraviolet high or intermediate energy field theory, but not yet to a lattice cutoff scale). The “gauge structure” can be compact, continuous, abelian or non-abelian. Our theory sits outside the paradigm of Maxwell electromagnetic theory in 1865 and Yang–Mills isospin/color theory in 1954. We discuss its local gauge transformation in terms of the ungauged vector-like or tensor-like higher-moment global symmetry. The non-abelian gauge structure is caused by gauging the non-commutative symmetries: a higher-moment symmetry and a charge conjugation (particle–hole) symmetry. Vector global symmetries along time direction may exhibit time crystals. We explore the relation of these long-range entangled matters to a non-abelian generalization of Fracton order in condensed matter, a field theory formulation of foliation, the spacetime embedding and Embeddon that we newly introduce, and possible fundamental physics applications to dark matter or dark energy.

36 MATERIALS SCIENCE↗