Evidence map›Paper›PMID 39938509›Full record

ArticleStructure (London, England : 1993)2025

Unique mechanisms to increase structural stability and enhance antigen binding in nanobodies.

Natalia E Ketaren, Peter C Fridy, Vladimir Malashkevich, Tanmoy Sanyal, Marc Brillantes, Mary K Thompson, Deena A Oren, Jeffrey B Bonanno, Andrej Šali, Steven C Almo and 2 more

Abstract read
In one paragraph

Article in Structure (London, England : 1993), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Review
  6. Nanobodies targeting hnRNPA2/B1 and tau.bioRxiv : the preprint server for biology · 2025
    Article
  7. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Natalia E KetarenLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: nketaren@rockefeller.edu.
Peter C FridyLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
Vladimir MalashkevichDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
Tanmoy SanyalDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
Marc BrillantesLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
Mary K ThompsonLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
Deena A OrenStructural Biology Resource Center, The Rockefeller University, New York, NY 10065, USA.
Jeffrey B BonannoDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
Andrej ŠaliDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
Steven C AlmoDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
Brian T ChaitLaboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
Michael P RoutLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: rout@rockefeller.edu.

Funding

The NYSGRC: A Large Scale Center for PSI:BiologyU54GM094662 · NIGMS · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI ALMO, STEVEN C. · 2010 to 2014
$32.6M
X-RAY STRUCTURE OF RIFM PROTEIN FROM THE BIOSYNTHESIS PATHWAY OF THE ANSAMYCIN AP41RR012408 · NCRR · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI SWEET, ROBERT M · 1998 to 2011
$32.2M
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Macromolecular Crystallography at the National Synchrotron Light SourceP41GM103473 · NIGMS · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI SWEET, ROBERT M · 2012 to 2013
$4.9M
Nucleocytoplasmic transport: a target for cellular controlU01GM098256 · NIGMS · ROCKEFELLER UNIVERSITY · PI AITCHISON, JOHN D., ROUT, MICHAEL P · 2011 to 2014
$3.0M
Synergistic Nanobodies for Pandemic PreparednessR01AI189657 · NIAID · ROCKEFELLER UNIVERSITY · PI JOHN D. AITCHISON, MICHAEL P ROUT · 2025 to 2026
$1.7M
Powassan virus nanobodies from camelid monomeric variable antibody domains elicited by natural infectionR21AI154180 · NIAID · ROCKEFELLER UNIVERSITY · PI MACDONALD, MARGARET R · 2020 to 2021
$466k
NCRR NIH HHS P41 RR012408NIAID NIH HHS R01 AI189657NIAID NIH HHS R21 AI154180NIGMS NIH HHS P41 GM103473NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM083960NIGMS NIH HHS U01 GM098256NIGMS NIH HHS U54 GM094662
6 · The paper itself

Abstract

Nanobodies are single domain antibody variants proving themselves to be compelling tools for research, disease diagnostics, and as therapeutics targeting a myriad of disease agents. However, despite this potential, their mechanisms of paratope presentation and structural stabilization have not been fully explored. Here, we show that unlike monoclonal antibodies, a nanobody repertoire maximizes sampling of an antigen surface by binding a single antigen in at least three different orientations, which are correlated with their paratope composition. Structure-guided reengineering of several nanobodies reveals that a single point mutation within the paratope or a highly conserved region of a nanobody's framework 3 (FR3) can markedly improve antigen affinity, nanobody stability, or both. Conversely, we show the negative impact on antigen affinity when "over-stabilizing" nanobodies. Collectively our results provide a universal strategy to tune a nanobody's affinity by modifying specific residues that can readily be applied to guide nanobody optimization and functionalization.

Indexed as

AntigensSingle-Domain AntibodiesAntibody AffinityBinding Sites, AntibodyHumansModels, MolecularPoint MutationProtein BindingProtein EngineeringProtein StabilityAntigensSingle-Domain Antibodiesantibodygreen fluorescent proteinnanobodynanobody engineeringnanobody optimizationSARS-CoV-2 nanobodiesV(H)H

Identifiers

PMID39938509
PMCPMC12042621

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.