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    Protein Science: Volume 33, Issue 3

    March 2024
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  • First Published: 14 February 2024
Cover Image

Conformational landscape of the 4-helix bundle HAMP signaling domain family represented by AlphaFold2 models. Each point represents a single model of a HAMP domain, with their relative positions reflecting structural similarity. The conformational landscape shows four basic motions that the HAMP domains can undergo and is colored according to each of these motions. For details, see: Aleksander Winski et al., Protein Science, 2023. https://doi.org/10.1002/pro.4846

Issue Information

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Issue information

  • First Published: 14 February 2024

RESEARCH ARTICLES

Open Access

Evidence of direct interaction between cisplatin and the caspase-cleaved prostate apoptosis response-4 tumor suppressor

Krishna K. Raut,  Samjhana Pandey,  Gyanendra Kharel,  Steven M. Pascal, 
  • First Published: 13 December 2023
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Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains

Sherry Wong,  Madeline E. West,  Gareth J. Morgan, 
  • First Published: 15 December 2023
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Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis

Shelby L. Heath,  Alex J. Guseman,  Angela M. Gronenborn,  W. Seth Horne, 
  • First Published: 25 December 2023
Free Access

Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior

Rainier-Numa Georges,  Lionel Ballut,  Guillaume Octobre,  Arnaud Comte,  Laurence Hecquet,  Franck Charmantray,  Bastien Doumèche, 
  • First Published: 25 December 2023
Open Access

Structural characterization of the Sel1-like repeat protein LceB from Legionella pneumophila

Tiffany V. Penner,  Neil Lorente Cobo,  Deepak T. Patel,  Dhruvin H. Patel,  Alexei Savchenko,  Ann Karen C. Brassinga,  Gerd Prehna, 
  • First Published: 31 December 2023
Open Access

The mineralocorticoid receptor forms higher order oligomers upon DNA binding

Gregory Fettweis,  Thomas A. Johnson,  Brian Almeida-Prieto,  Julián Weller-Pérez,  Diego M. Presman,  Gordon L. Hager,  Diego Alvarez de la Rosa, 
  • First Published: 31 December 2023
Free Access

The effects of biological crowders on fibrillization, structure, diffusion, and conformational dynamics of α-synuclein

Sina Heravi,  Jude Vincent Dobbin Power,  Anand Yethiraj,  Valerie Booth, 
  • First Published: 15 February 2024
Free Access

Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution

Nooriel E. Banayan,  Blaine J. Loughlin,  Shikha Singh,  Farhad Forouhar,  Guanqi Lu,  Kam-Ho Wong,  Matthew Neky,  Henry S. Hunt,  Larry B. Bateman Jr,  Angel Tamez,  Samuel K. Handelman,  W. Nicholson Price,  John F. Hunt, 
  • First Published: 15 February 2024
Open Access

Discovery of broadly-neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens

Esperanza Rivera-de-Torre,  Stefanos Lampadariou,  Mark Møiniche,  Markus F. Bohn,  Seyed Mahdi Kazemi,  Andreas H. Laustsen, 
  • First Published: 15 February 2024

REVIEW ARTICLES

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Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants

Artur Meller,  Devin Kelly,  Louis G. Smith,  Gregory R. Bowman, 
  • First Published: 15 February 2024

RESEARCH ARTICLES

Open Access

Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy

Yasmin Ben-Ishay,  Yoav Barak,  Akiva Feintuch,  Olivier Ouari,  Annalisa Pierro,  Elisabetta Mileo,  Xun-Cheng Su,  Daniella Goldfarb, 
  • First Published: 15 February 2024
Free Access

Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening

Yong Yao Loh,  Jothi Anantharajan,  Qiwei Huang,  Weijun Xu,  Justina Fulwood,  Hui Qi Ng,  Elizabeth Yihui Ng,  Chong Yu Gea,  Meng Ling Choong,  Qian Wen Tan,  Xiaoying Koh,  Wan Hsin Lim,  Kassoum Nacro,  Joseph Cherian,  Nithya Baburajendran,  Zhiyuan Ke,  CongBao Kang, 
  • First Published: 15 February 2024

TOOLS FOR PROTEIN SCIENCE

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Protein ensemble modeling and analysis with MMMx

Gunnar Jeschke, 
  • First Published: 15 February 2024

RESEARCH ARTICLES

Open Access

The ratio of fibroin to sericin in the middle silk gland of Bombyx mori and its correlation with the extensional behavior of the silk dope

Teemu Välisalmi,  Markus B. Linder, 
  • First Published: 21 February 2024

METHODS AND APPLICATIONS

Open Access

Modeling membrane geometries implicitly in Rosetta

Hope Woods,  Julia Koehler Leman,  Jens Meiler, 
  • First Published: 15 February 2024

TOOLS FOR PROTEIN SCIENCE

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Accounting for nonuniformity of bulk-solvent: A mosaic model

Pavel V. Afonine,  Paul D. Adams,  Oleg V. Sobolev,  Alexandre G. Urzhumtsev, 
  • First Published: 15 February 2024

METHODS AND APPLICATIONS

Open Access

Controlling the incorporation of fluorinated amino acids in human cells and its structural impact

Azzurra Costantino,  Lan B. T. Pham,  Letizia Barbieri,  Vito Calderone,  Gili Ben-Nissan,  Michal Sharon,  Lucia Banci,  Enrico Luchinat, 
  • First Published: 15 February 2024

TOOLS FOR PROTEIN SCIENCE

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Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families

Dariia Yehorova,  Rory M. Crean,  Peter M. Kasson,  Shina C. L. Kamerlin, 
  • First Published: 15 February 2024

RESEARCH ARTICLES

Open Access

The C-terminus is essential for the stability of the mycobacterial channel protein MspA

Mikhail Pavlenok,  Rashmi Ravindran Nair,  R. Curtis Hendrickson,  Michael Niederweis, 
  • First Published: 15 February 2024
Free Access

Protective roles of highly conserved motif 1 in tardigrade cytosolic-abundant heat soluble protein in extreme environments

Donguk Kang,  Min June Yang,  Hwan Kim,  Chin-Ju Park, 
  • First Published: 15 February 2024
Free Access

A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling

Massimo Bellanda,  Milena Damulewicz,  Barbara Zambelli,  Elisa Costanzi,  Francesco Gregoris,  Stefano Mammi,  Silvio C. E. Tosatto,  Rodolfo Costa,  Giovanni Minervini,  Gabriella M. Mazzotta, 
  • First Published: 15 February 2024
Open Access

Crystal structure of the tegument protein UL82 (pp71) from human cytomegalovirus

Jan Eberhage,  Ian P. Bresch,  Ramya Ramani,  Niklas Viohl,  Thalea Buchta,  Christopher L. Rehfeld,  Petra Hinse,  Thomas F. Reubold,  Melanie M. Brinkmann,  Susanne Eschenburg, 
  • First Published: 15 February 2024
Open Access

The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation

Markus Schweipert,  Thomas Nehls,  Anton Frühauf,  Cecilé Debarnot,  Adarsh Kumar,  Stefan Knapp,  Frederik Lermyte,  Franz-Josef Meyer-Almes, 
  • First Published: 15 February 2024

RESEARCH NOTE

Free Access

An intein-based biosensor to measure protein stability in vivo

Ahyun Son,  John S. Smetana,  Scott Horowitz,  Christopher W. Lennon, 
  • First Published: 21 February 2024

RESEARCH ARTICLES

Open Access

Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novo TIM barrels

Johanna-Sophie Koch,  Sergio Romero-Romero,  Birte Höcker, 
  • First Published: 21 February 2024
Free Access

A sequence-based model for identifying proteins undergoing liquid–liquid phase separation/forming fibril aggregates via machine learning

Shaofeng Liao,  Yujun Zhang,  Xinchen Han,  Tinglan Wang,  Xi Wang,  Qinglin Yan,  Qian Li,  Yifei Qi,  Zhuqing Zhang, 
  • First Published: 21 February 2024
Open Access

VWD domain stabilization by autocatalytic Asp-Pro cleavage

Noa Yeshaya,  Prashant Kumar Gupta,  Orly Dym,  David Morgenstern,  Dan Thomas Major,  Deborah Fass, 
  • First Published: 21 February 2024
Open Access

Structural insights into peptidoglycan glycosidase EtgA binding to the inner rod protein EscI of the type III secretion system via a designed EscI-EtgA fusion protein

J. Boorman,  X. Zeng,  J. Lin,  F. van den Akker, 
  • First Published: 21 February 2024
Open Access

Degradation versus fibrillogenesis, two alternative pathways modulated by seeds and glycosaminoglycans

Guglielmo Verona,  Sara Raimondi,  Diana Canetti,  P. Patrizia Mangione,  Loredana Marchese,  Alessandra Corazza,  Francesca Lavatelli,  Julian D. Gillmore,  Graham W. Taylor,  Vittorio Bellotti,  Sofia Giorgetti, 
  • First Published: 21 February 2024

TOOLS FOR PROTEIN SCIENCE

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Protein structure accuracy estimation using geometry-complete perceptron networks

Alex Morehead,  Jian Liu,  Jianlin Cheng, 
  • First Published: 21 February 2024

RESEARCH ARTICLES

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Common evolutionary origins of the bacterial glycyl tRNA synthetase and alanyl tRNA synthetase

Claudia Alvarez-Carreño,  Marcelino Arciniega,  Lluís Ribas de Pouplana,  Anton S. Petrov,  Adriana Hernández-González,  Jorge-Uriel Dimas-Torres,  Marco Igor Valencia-Sánchez,  Loren Dean Williams,  Alfredo Torres-Larios, 
  • First Published: 27 November 2023
Open Access

Direct evidence of lipid transport by the Drs2–Cdc50 flippase upon truncation of its terminal regions

Sara Abad Herrera,  Bo Højen Justesen,  Thibaud Dieudonné,  Cédric Montigny,  Poul Nissen,  Guillaume Lenoir,  Thomas Günther Pomorski, 
  • First Published: 08 December 2023
Open Access

Exploring the conformational changes of the Munc18-1/syntaxin 1a complex

Ioanna Stefani,  Justyna Iwaszkiewicz,  Dirk Fasshauer, 
  • First Published: 18 December 2023
Open Access

Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations

Matteo Castelli,  Andrea Magni,  Giorgio Bonollo,  Silvia Pavoni,  Francesco Frigerio,  A. Sofia F. Oliveira,  Fabrizio Cinquini,  Stefano A. Serapian,  Giorgio Colombo, 
  • First Published: 25 December 2023