Publications

U54 Bibliography April_2024

U54_Bibliography_April_2024_.docx

Hot off the Press!

Links to our recent publications!

Awesome insights into the structural dynamics of HIV-1 Envelop pre-fusion states

microdynamics

Microsecond dynamics control the HIV-1 envelope conformation

Ashley L. Bennett1, R.J. Edwards1, Irina Kosheleva2, Carrie Saunders1, Yishak Bililign1,
Ashliegh Williams1, Katayoun Manosouri1, Kevin O. Saunders1,3, Barton F. Haynes 1,4,5,
Priyamvada Acharya1,3,5, Rory Henderson1,6
 

1Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
2BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South
  Cass Ave, Bld 434B, Lemont, IL 60439, USA.
3Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.
4Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.
5Department of Biochemistry, Duke University, Durham, NC 27710, USA
6Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA

 

Figure 1_cell_Sanders 2024

Vaccine induction of CD4-mimicking broadly neutralizing antibody precursors in macaques

Kevin O. Saunders1,2,3,4,14, James Counts1,5, Victoria Stalls1,5 , Robert Edwards1,5, Kartik5, Manne1,5, Xiaozhi Lu1,5, Bhishem Thakur1,5, Katayoun Mansouri1,5 , Yue Chen1,5 , Rob Parks1,5, Maggie Barr1,5, Laura Sutherland1,5, Joena Bal1,5, Nicholas Havill1,6, Haiyan Chen1,5, Emily Machiele1,5, Nolan Jamieson1,5, Bhavna Hora1,5, Megan Kopp1,5, Katarzyna Janowska1,5, Kara Anasti1,5, Chuancang Jiang1,5, Sravani Venkatayogi 1,5, Amanda Eaton1,5, Rory Henderson1,5, Christopher Barbosa7, S. Munir Alam1,5, Sampa Santra8, Drew Weissman9,10, M. Anthony Moody1,11 , Derek W. Cain1,5, Ying Tam7, Mark Lewis12, Wilton B. Williams1,2,3 , Kevin Wiehe1,5 , David Montefiori1,2, Priyamvada Acharya 1,2,13 , Barton F. Haynes1,3,4,5.

 

1   Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710,USA.
2   Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
3   Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
4   Department of Molecular Genetics and Microbiology, Duke University School of Medicine,
5   Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
6   Department of Biology, Davidson College, Davidson, NC 28035, USA
7   Acuitas LLC, Vancouver, BC
8   Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
9   Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
10 Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
11 Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA.
12 BIOQUAL, Rockville, MD 20850, USA.
13 Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.
14 Lead contact

nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography

Bartesaghi_LinkedIn Newsletter

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Researchers in the Duke Center for HIV Structural Biology and MIT have developed and validated a novel, high-throughput approach for structure determination by single-particle cryo-electron tomography using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP.

Check out the full article by Dr. Hsuan-Fu Liu et al, in Nature Methods!

Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage

 

DH270 clone phylogenetic tree depicting cryo-EM maps determined for each clonalmember Fab bound to the CH848 d949 trimer (white).
Modified Figure 1. V3-glycan targeting DH270 bnAb phylogeny.

The inferred DH270 clone phylogenetic tree depicting cryo-EM maps determined for each clonal member Fab bound to the CH848 d949 trimer (white). The clonal member names are colored according to the Fab color of each map.

Check out the full article by Rory Henderson et al. in Nature Communications!

Structures of Langya Virus Fusion Protein Ectodomain in Pre- and Postfusion Conformation

LayV FP Comp
Modified Supplemental Figure 4: Fusion peptide comparison.

Comparison of fusion peptide location in a selected group of viral fusion proteins. In the top portion of each panel, fusion proteins are shown in cartoon representation in gray, with the fusion peptide as orange spheres, and in the bottom portion, fusion peptides are shown as cartoon representation with side chains as sticks, orange, with the surface of the rest of the fusion protein colored based on protomer.

Check out the full article by Aaron May et al. in the Journal of Virology!

Pre-Prints

medrxiv_logo

Vaccine Induction in Humans of Polyclonal HIV-1 Heterologous Neutralizing Antibodies



Wilton B. Williams1,2,5,*&, S. Munir Alam1,4,*&, Gilad Ofek3,15,&, Nathaniel Erdmann9,&, David
Montefiori1,2,&, Michael Seaman12, Kshitij Wagh14, Bette Korber14, Robert J. Edwards1,4,
Katayoun Mansouri1, Amanda Eaton2, Derek W. Cain1,4, Robert Parks1, Maggie Barr1, Mitchell
Martin1, Jongln Hwang1, Andrew Foulger1, Kara Anasti1, Salam Sammour1, Xiao Huang1, Jared
Lindenberger1, Katarzyna Janowska1, Aurelie Niyongabo3, Benjamin M. Janus3,15, Anagh
Astavans3, Christopher Fox13, Ipsita Mohanty1, Tyler Evangelous1, Madison Berry1, Helene
Kirshner1, Kevin Saunders1,2,5,6, Kevin Wiehe1,4, Kristen Cohen7, M. Juliana McElrath7,
Lawrence Corey7, Priyamvada Acharya1,2,10, Stephen R. Walsh8,*, Lindsey R. Baden8,* and
Barton F. Haynes1,4,5,11,*.


1Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710
2Department of Surgery, Duke School of Medicine, Durham, NC 27710
3Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
4Department of Medicine, Duke School of Medicine, Durham, NC 27710
5Department of Immunology, Duke School of Medicine, Durham, NC 27710
6Department of Molecular Genetics and Microbiology, Duke School of Medicine, Durham, NC 27710
7Fred Hutchinson Cancer Research Center, Seattle WA 98109
8Brigham and Women’s Hospital, Harvard Medical School, Boston MA 02115
9University of Alabama Medical Center, Birmingham AL 35223
10Department of Biochemistry, Duke School of Medicine, Durham, NC 27710
11Duke Global Health Institute, Duke School of Medicine, Durham, NC 27710
12Beth Israel Deaconess Medical Center, Harvard Medical School, Boston MA 02215
13Access to Access to Advanced Health Institute, Seattle WA, 98102
14Los Alamos National Laboratory, Los Alamos NM, 87545
15Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville MD 20850
&These authors contributed equally to this work.
*Corresponding Authors: wilton.williams@duke.edu; munir.alam@duke.edu;
barton.haynes@duke.edu; lbaden@bwh.harvard.edu; SWALSH@bwh.harvard.edu.

 

BioRxiv_logo 2023

Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted/ founder (TF) sensitivity to broadly neutralizing antibodies


Durgadevi Parthasarathy1,10, Karunakar Reddy Pothula3,10, Kim-Marie A. Dam2, Sneha Ratnapriya1, Héctor Cervera Benet1, Ruth Parsons3, Xiao Huang3 , Salam Sammour3, Katarzyna
Janowska3, Miranda Harris1, Samuel Sacco2,11, Joseph Sodroski4, Michael D. Bridges5,6, Wayne L. Hubbell5,6, Priyamvada Acharya3,7 and Alon Herschhorn1,8,9 *


1 Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
2 Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
3 Duke Human Vaccine Institute, Durham, NC, USA
4 Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of  Microbiology, Harvard Medical School, Boston, MA, USA
5 Jules Stein Eye Institute, University of California, Los Angeles, CA, USA
6 Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
7 Department of Surgery, and Department of Biochemistry, Duke University, Durham, NC, USA
8 Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
9 Microbiology, Immunology, and Cancer Biology Graduate Program; The College of Veterinary Medicine
  Graduate Program; and the Molecular Pharmacology and Therapeutics Graduate Program, University of
  Minnesota, Minneapolis, MN, USA
10 These authors contributed equally:  Durgadevi Parthasarathy, Karunakar Reddy Pothula.
11 Present address: Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa
Cruz, CA, USA

 


*Correspondence:
Alon Herschhornl: aherschh@umn.edu

An intact amber-free HIV-1 system for in-virus protein bioorthogonal click labeling that delineates envelope conformational dynamics

Yuanyun Ao1, Jonathan R. Grover2, Yang Han1, Guohua Zhong1, Wenyi Qin1, Dibya
Ghimire1, Md. Anzarul Haque1, Rajanya Bhattacharjee3,4, Baoshan Zhang5, James
Arthos6, Edward A. Lemke3,4, Peter D. Kwong5, *Maolin Lu1


1Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, Texas, USA
2Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
3Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg–University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz, Germany
4Institute of Molecular Biology, Ackermannweg 4, Mainz, Germany
5Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
6Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
*Correspondence should be addressed to M.L.: maolin.lu@uthct.edu