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    Protein Science: Volume 34, Issue 6

    June 2025
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  • First Published: 12 May 2025
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Forces visualized as field lines around the enzyme guanylate kinase show how BioSpring's interactive simulations steer a ligand, modeled as an elastic network with non-bonded interactions, into low-energy states. For details, see: Benoist Laurent, et al., Protein Science, 2025. https://doi.org/10.1002/pro.70130

Issue Information

Free Access

Issue information

  • First Published: 12 May 2025

RESEARCH ARTICLE

Open Access

Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation

Amanda D. Due,  Norman E. Davey,  F. Emil Thomasen,  Nicholas Morffy,  Andreas Prestel,  Inna Brakti,  Charlotte O'Shea,  Lucia C. Strader,  Kresten Lindorff-Larsen,  Karen Skriver,  Birthe B. Kragelund, 
  • First Published: 15 May 2025
Open Access

Chemically induced partial unfolding of the multifunctional apurinic/apyrimidinic endonuclease 1

Ratan Rai,  Olabode I. Dawodu,  Jingwei Meng,  Steven M. Johnson,  Jonah Z. Vilseck,  Mark R. Kelley,  Joshua J. Ziarek,  Millie M. Georgiadis, 
  • First Published: 15 May 2025
Open Access

Phosphorylation of ITIM motifs drives the structural transition of indoleamine 2,3-dioxygenase 1 between enzymatic and non-enzymatic states

Gyula Hoffka,  Lilla Hornyák,  Lóránt Székvölgyi,  Márton Miskei, 
  • First Published: 15 May 2025
Open Access

Modulation of insulin aggregation by betaine and proline directly observed via real-time super-resolution microscopy

Steen W. B. Bender,  Jacob Kæstel-Hansen,  Vito Foderà,  Nikos S. Hatzakis,  Min Zhang, 
  • First Published: 15 May 2025

RECOLLECTIONS

Open Access

Unlocking complexity through neutron scattering: Structure and dynamics of protein–polymer conjugates

Daniela Russo,  Frederik Wurm,  Jose Teixeira, 
  • First Published: 19 May 2025

REVIEW ARTICLE

Open Access

Experimental methods for studying amyloid cross-interactions

Aleksandra Kalitnik,  Anna Lassota,  Oliwia Polańska,  Marlena Gąsior-Głogowska,  Monika Szefczyk,  Agnieszka Barbach,  Jarosław Chilimoniuk,  Izabela Jęśkowiak-Kossakowska,  Alicja W. Wojciechowska,  Jakub W. Wojciechowski,  Natalia Szulc,  Małgorzata Kotulska,  Michał Burdukiewicz, 
  • First Published: 19 May 2025

RESEARCH ARTICLE

Open Access

Polyglutamine expansion induced dynamic misfolding of androgen receptor

Laurens W. H. J. Heling,  Vahid Sheikhhassani,  Julian Ng,  Morris van Vliet,  Alba Jiménez-Panizo,  Andrea Alegre-Martí,  Jaie Woodard,  Willeke van Roon-Mom,  Iain J. McEwan,  Eva Estébanez-Perpiñá,  Alireza Mashaghi, 
  • First Published: 15 May 2025
Open Access

Using a stable protein scaffold to display peptides that bind to alpha-synuclein fibrils

Samuel Bismut,  Matthias M. Schneider,  Masashi Miyasaki,  Yuqing Feng,  Ellis J. Wilde,  M. Dylan Gunawardena,  Tuomas P. J. Knowles,  Gabrielle S. Kaminski Schierle,  Laura S. Itzhaki,  Janet R. Kumita, 
  • First Published: 15 May 2025
Open Access

Binding free energy analysis of galectin-3 natural ligands and synthetic inhibitors

Luke Newman,  Valerie Vaissier Welborn, 
  • First Published: 22 May 2025
Full Access

Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations

Yuan-Wei Ma,  Guan-Fang Wang,  Hong-Yi Chen,  Min-Yeh Tsai, 
  • First Published: 15 May 2025
Full Access

Extrinsic and intrinsic factors affect copper-induced protein precipitation across eukaryotic and prokaryotic proteomes

Grace R. Sturrock,  Amy T. R. Robison,  Azim Dharani,  Eric E. Monson,  Katherine J. Franz,  Michael C. Fitzgerald, 
  • First Published: 15 May 2025
Open Access

A quantitative comparison of the deleteriousness of missense and nonsense mutations using the structurally resolved human protein interactome

Ting-Yi Su,  Yu Xia, 
  • First Published: 19 May 2025
Open Access

CXXC5 is a ubiquitinated protein and is degraded by the ubiquitin-proteasome pathway

Hazal Ayten,  Pelin Toker,  Gizem Turan Duman,  Çağla Ece Olgun,  Öykü Deniz Demiralay,  Büşra Bınarcı,  Gizem Güpür,  Pelin Yaşar,  Hesna Begüm Akman,  Per Haberkant,  Mesut Muyan, 
  • First Published: 15 May 2025
Open Access

Molecular characterization of a synthetic neutralizing antibody targeting p67 of Theileria parva

Shane Miersch,  Alex U. Singer,  Chao Chen,  Fred Fellouse,  Anupriya Gopalsamy,  Luciano Silva e Costa,  Anna Lacasta,  Hannah Chege,  Naomi Chege,  Vishvanath Nene,  Sachdev S. Sidhu, 
  • First Published: 19 May 2025
Open Access

Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15

Spyros D. Chatziefthymiou,  Maria Kuzikov,  Sara Afandi,  Greta Kovacs,  Sukrit Srivastava,  Andrea Zaliani,  Andrey Gruzinov,  Guillaume Pompidor,  Michele Lunelli,  Golam Rizvee Ahmed,  Jörg Labahn,  Johanna Hakanpää,  Björn Windshügel,  Michael Kolbe, 
  • First Published: 15 May 2025
Full Access

Investigating the unbinding mechanisms and kinetics of MmpL3 inhibitors: A computational study

Likun Zhao,  Xiuling Ma,  Bo Liu,  Xiaojun Yao,  Huanxiang Liu,  Qianqian Zhang, 
  • First Published: 15 May 2025

TOOLS FOR PROTEIN SCIENCE

Full Access

Enhanced protein extraction and quantification protocol for microsamples: An ultra-sensitive workflow for low-volume, low-concentration total protein lysates

Taylor Wilcox,  Michael E. Widlansky,  Justin Westhoff,  Jingli Wang,  Rong Ying,  Abigail Thorgerson,  Michelle L. Roberts, 
  • First Published: 15 May 2025

RESEARCH ARTICLE

Open Access

Design and evolution of a synthetic small protein scaffold based on the WW domain

Ana Margarida Gonçalves Carvalho Dias,  Gonçalo Duarte Gomes Teixeira,  Arménio Jorge Moura Barbosa,  Joao Goncalves,  Olga Iranzo,  Ana Cecília Afonso Roque, 
  • First Published: 22 May 2025

TOOLS FOR PROTEIN SCIENCE

Open Access

GRU4ACE: Enhancing ACE inhibitory peptide prediction by integrating gated recurrent unit with multi-source feature embeddings

Saeed Ahmed,  Nalini Schaduangrat,  Pramote Chumnanpuen,  Watshara Shoombuatong, 
  • First Published: 15 May 2025

RESEARCH ARTICLE

Open Access

Functional implications of hexameric dynamics in SARS-CoV-2 Nsp15

Manashi Sonowal,  Gihan Ketawala,  Nirupa Nagaratnam,  Dhenugen Logeswaran,  Shibom Basu,  Daniele de Sanctis,  Julien Orlans,  Samuel L. Rose,  Rebecca J. Jernigan,  Hao Hu,  Jose Domingo Meza Aguilar,  Madurangi E. Ranaweera,  Michele A. Zacks,  Julian J.-L. Chen,  Debra T. Hansen,  Lynn G. Schrag,  Raimund Fromme,  Sabine Botha,  Petra Fromme, 
  • First Published: 24 May 2025
Full Access

Enhanced secretion through type 1 secretion system by grafting a calcium-binding sequence to modify the folding of cargo proteins

Ryo Uehara,  Yuka Kamiya,  Shuta Maeda,  Keisuke Okamoto,  Shuntaro Toya,  Ryohei Chiba,  Hiroshi Amesaka,  Kazufumi Takano,  Hiroyoshi Matsumura,  Shun-ichi Tanaka, 
  • First Published: 19 May 2025

RESEARCH NOTE

Open Access

Inhibition of tau aggregation by the CCT3 and CCT7 apical domains

Miki Ben-Maimon,  Nadav Elad,  Segev Naveh-Tassa,  Yaakov Levy,  Amnon Horovitz, 
  • First Published: 22 May 2025

TOOLS FOR PROTEIN SCIENCE

Open Access

MultiPassMerger: Automated data processing for multipass cyclic ion mobility HDX-MS

Vanessa Duerr,  Damon Griffiths,  Argyris Politis, 
  • First Published: 24 May 2025

REVIEW ARTICLE

Full Access

Prion diseases: Lessons from historical outbreaks and potential emerging ones

Aidan P. Holman,  Dmitry Kurouski, 
  • First Published: 24 May 2025

RESEARCH ARTICLE

Open Access

De novo design of ATPase based on a blueprint optimized for harboring the P-loop motif

Takahiro Kosugi,  Mikio Tanabe,  Nobuyasu Koga, 
  • First Published: 13 May 2025
Open Access

Mechanisms of helix induction by the closed loop

Yuuki Yanagida,  Kiyomi Yoshida,  Mio Ohtomo,  Kazuo Fujiwara,  Masamichi Ikeguchi, 
  • First Published: 19 May 2025
Open Access

The enterobactin biosynthetic intermediate 2,3-dihydroxybenzoic acid is a competitive inhibitor of the Escherichia coli isochorismatase EntB

Xue Bin,  Peter D. Pawelek, 
  • First Published: 22 May 2025

TOOLS FOR PROTEIN SCIENCE

Open Access

3-D substructure search by transitive closure in AlphaFold database

Hao Liu,  Aleksi Laiho,  Petri Törönen,  Liisa Holm, 
  • First Published: 22 May 2025
Open Access

AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes

Minal Khatri,  N. R. Siva Shanmugam,  Xinpeng Zhang,  Revanth Sai Kumar Reddy Patel,  Yanbin Yin, 
  • First Published: 22 May 2025

RESEARCH ARTICLE

Open Access

New glycoside hydrolase families of β-1,2-glucanases

Masahiro Nakajima,  Nobukiyo Tanaka,  Sei Motouchi,  Kaito Kobayashi,  Hisaka Shimizu,  Koichi Abe,  Naoya Hosoyamada,  Naoya Abara,  Naoko Morimoto,  Narumi Hiramoto,  Ryosuke Nakata,  Akira Takashima,  Marie Hosoki,  Soichiro Suzuki,  Kako Shikano,  Takahiro Fujimaru,  Shiho Imagawa,  Yukiya Kawadai,  Ziyu Wang,  Yoshinao Kitano,  Takanori Nihira,  Hiroyuki Nakai,  Hayao Taguchi, 
  • First Published: 24 May 2025

RESEARCH NOTE

Open Access

A single buried cysteine acts as a hydrophobic stabilizer of a folding intermediate and transition state in the MATH domain of SPOP

Livia Pagano,  Awa Diop,  Valeria Pennacchietti,  Mariana Di Felice,  Eduarda S. Ventura,  Julian Toso,  Angelo Toto,  Stefano Gianni, 
  • First Published: 14 May 2025

RESEARCH ARTICLE

Open Access

Identifying and quantifying membrane interactions of the protein human cis-prenyltransferase

Duncan M. Boren,  Shiri Kredi,  Ekaterina Positselskaya,  Moshe Giladi,  Yoni Haitin,  Josh V. Vermaas, 
  • First Published: 24 May 2025
Full Access

Protein–RNA condensation kinetics via filamentous nanoclusters

Ramon Peralta-Martinez,  Araceli Visentin,  Mariano Salgueiro,  Silvia Susana Borkosky,  Mariana Araujo Ajalla Aleixo,  Rodrigo Villares Portugal,  Ignacio Enrique Sanchez,  Gonzalo Prat-Gay, 
  • First Published: 24 May 2025
Open Access

The mycotoxin Beauvericin is an uncompetitive inhibitor of Cathepsin B

Xiaoli Yang,  Pablo Cea-Medina,  Mohanraj Gopalswamy,  Aparna Vaidya,  Sonja Schavier,  Shixin Oltzen,  Sofie Moßner,  Anfei Huang,  Jing Qi,  Johanna Maria Hölken,  Nicole Teusch,  Doreen M. Floss,  Markus Uhrberg,  Holger Gohlke,  Stefanie Scheu, 
  • First Published: 24 May 2025
Open Access

Enhancing schistosomiasis drug discovery approaches with optimized proteasome substrates

Elany B. Silva,  Zhenze Jiang,  Chenxi Liu,  Pavla Fajtová,  Thaiz R. Teixeira,  Giovana de Castro Fiorini Maia,  Lawrence J. Liu,  Nelly El-Sakkary,  Danielle E. Skinner,  Ali Syed,  Steven C Wang,  Conor R. Caffrey,  Anthony J. O'Donoghue, 
  • First Published: 24 May 2025
Open Access

Cis-nonProline peptides: Genuine occurrences and their functional roles

Jane S. Richardson,  Lizbeth L. Videau,  Christopher J. Williams,  Bradley J. Hintze,  Steven M. Lewis,  David C. Richardson, 
  • First Published: 24 May 2025
Open Access

Synthetic antibodies targeting EphA2 induce diverse signaling-competent clusters with differential activation

Jarrett J. Adams,  Heather A. Bruce,  Suryasree Subramania,  Lynda Ploder,  Julia Garcia,  Isabelle Pot,  Levi L. Blazer,  Alexander U. Singer,  Sachdev S. Sidhu, 
  • First Published: 24 May 2025
Open Access

Project automation in CCP4 Cloud: Enabling customization and high-throughput efficiency

Eugene Krissinel,  Maria Fando,  Oleg Kovalevskiy,  Ronan Keegan,  Jools Wills,  Andrey Lebedev,  Ville Uski,  Charles Ballard, 
  • First Published: 24 May 2025
Open Access

Defining short linear motif binding determinants by phage display-based deep mutational scanning

Caroline Benz,  Lars Maassen,  Leandro Simonetti,  Filip Mihalic,  Richard Lindqvist,  Ifigenia Tsitsa,  Aimiliani Konstantinou,  Per Jemth,  Anna K. Överby,  Norman E. Davey,  Ylva Ivarsson, 
  • First Published: 24 May 2025
Open Access

Lysine acetylation modulates s-OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling

Javaid Jabbar,  Bakht Afroze,  Naomi X. Y. Ling,  Jonathan S. Oakhill,  Isabelle Rouiller, 
  • First Published: 29 May 2025

RESEARCH NOTE

Full Access

Cryo-EM structures of engineered Shiga toxin-based immunogens capable of eliciting neutralizing antibodies with therapeutic potential against hemolytic uremic syndrome

Alejandro Ezequiel Cristófalo,  Arvind Sharma,  María Laura Cerutti,  Kedar Sharma,  Roberto Melero,  Romina Pardo,  Fernando Alberto Goldbaum,  Mario Borgnia,  Vanesa Zylberman,  Lisandro Horacio Otero, 
  • First Published: 24 May 2025

RESEARCH ARTICLE

Full Access

The WRC domain of GRF transcription factors: Structure and DNA recognition

Franco A. Biglione,  Nahuel D. González Schain,  Javier F. Palatnik,  Rodolfo M. Rasia, 
  • First Published: 29 May 2025