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    Protein Science: Volume 33, Issue 4

    April 2024
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Cover Image

  • First Published: 18 March 2024
Cover Image

Superposed ccGFP E6 (orange) and ccGFP 8 (blue) in cartoon representation centered at R70 showing the side-chain rotamer differences of R70 between ccGFP E6 and the other variants (represented by ccGFP 8). For details, see: Li-Wei Hung et al., Protein Science, 2023. https://doi.org/10.1002/pro.4886

Issue Information

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Issue information

  • First Published: 18 March 2024

RESEARCH ARTICLES

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Biochemical and structural characterization reveals Rv3400 codes for β-phosphoglucomutase in Mycobacterium tuberculosis

Latika Singh,  Subramanian Karthikeyan,  Krishan Gopal Thakur, 
  • First Published: 19 March 2024
Free Access

Classifying protein kinase conformations with machine learning

Ivan Reveguk,  Thomas Simonson, 
  • First Published: 19 March 2024

RESEARCH NOTE

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Cell surface β-lactamase recruitment: A facile selection to identify protein–protein interactions

Jordan A. Hinmon,  Jade M. King,  Latrina J. Mayo,  Cierra R. Faries,  Ya'hnis T. Lockett,  David W. Crawford,  Patrick C. Beardslee,  Alexander Hendricks,  Brian R. McNaughton, 
  • First Published: 19 March 2024

RESEARCH ARTICLES

Open Access

RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases

Di Zhang,  Honorata Czapinska,  Matthias Bochtler,  Alexander Wlodawer,  Jacek Lubkowski, 
  • First Published: 19 March 2024
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Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer

Kristína Felčíková,  Andrej Hovan,  Marek Polák,  Dmitry S. Loginov,  Veronika Holotová,  Carlos Díaz,  Tibor Kožár,  One-Sun Lee,  Rastislav Varhač,  Petr Novák,  Gregor Bánó,  Erik Sedlák, 
  • First Published: 19 March 2024

TOOLS FOR PROTEIN SCIENCE

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Xplor-NIH: Better parameters and protocols for NMR protein structure determination

Guillermo A. Bermejo,  Nico Tjandra,  G. Marius Clore,  Charles D. Schwieters, 
  • First Published: 19 March 2024

RESEARCH ARTICLES

Open Access

Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63

Iva Sučec,  Yanina Pankratova,  Mriganka Parasar,  Mei Hong, 
  • First Published: 19 March 2024
Open Access

Dual-wield NTPases: A novel protein family mined from AlphaFold DB

Koya Sakuma,  Ryotaro Koike,  Motonori Ota, 
  • First Published: 19 March 2024
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The dynamics of the flavin, NADPH, and active site loops determine the mechanism of activation of class B flavin-dependent monooxygenases

Gustavo Pierdominici-Sottile,  Juliana Palma,  María Leticia Ferrelli,  Pablo Sobrado, 
  • First Published: 19 March 2024
Open Access

The structural landscape of the immunoglobulin fold by large-scale de novo design

Jorge Roel-Touris,  Lourdes Carcelén,  Enrique Marcos, 
  • First Published: 19 March 2024
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A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features

Chao Chen,  Hongwu Yang,  Sheng Dong,  Cai You,  Sarah Moraïs,  Edward A. Bayer,  Ya-Jun Liu,  Jinsong Xuan,  Qiu Cui,  Itzhak Mizrahi,  Yingang Feng, 
  • First Published: 19 March 2024

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Examining evolutionary scale modeling-derived different-dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow

Karla L. Martínez-Mauricio,  César R. García-Jacas,  Greneter Cordoves-Delgado, 
  • First Published: 19 March 2024

RESEARCH ARTICLES

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Assessing the mechanism of fast-cycling cancer-associated mutations of Rac1 small Rho GTPase

Angela Parise,  Alessandra Magistrato, 
  • First Published: 19 March 2024
Open Access

Labile assembly of a tardigrade protein induces biostasis

S. Sanchez-Martinez,  K. Nguyen,  S. Biswas,  V. Nicholson,  A. V. Romanyuk,  J. Ramirez,  S. Kc,  A. Akter,  C. Childs,  E. K. Meese,  E. T. Usher,  G. M. Ginell,  F. Yu,  E. Gollub,  M. Malferrari,  F. Francia,  G. Venturoli,  E. W. Martin,  F. Caporaletti,  G. Giubertoni,  S. Woutersen,  S. Sukenik,  D. N. Woolfson,  A. S. Holehouse,  T. C. Boothby, 
  • First Published: 19 March 2024
Open Access

Engineering of IF1-susceptive bacterial F1-ATPase

Yuichiro C. Hatasaki,  Ryohei Kobayashi,  Ryo R. Watanabe,  Mayu Hara,  Hiroshi Ueno,  Hiroyuki Noji, 
  • First Published: 19 March 2024
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Construction of a versatile fusion protein for targeted therapy and immunotherapy

Xiu-Song Huang,  Li-Ting Yang,  Ke Yang,  Hang Zhou,  Tuersunayi Abudureheman,  Wei-Wei Zheng,  Kai-Ming Chen,  Cai-Wen Duan, 
  • First Published: 19 March 2024

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Adaptable SEC-SAXS data collection for higher quality structure analysis in solution

Tsutomu Matsui,  Ivan Rajkovic,  Blaine H. M. Mooers,  Ping Liu,  Thomas M. Weiss, 
  • First Published: 19 March 2024

RESEARCH ARTICLES

Open Access

Identification of a novel DNA repair inhibitor using an in silico driven approach shows effective combinatorial activity with genotoxic agents against multidrug-resistant Escherichia coli

Lorenzo Bernacchia,  Antoine Paris,  Arya Gupta,  Robert J. Charman,  Jake McGreig,  Mark N. Wass,  Neil M. Kad, 
  • First Published: 19 March 2024
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Unraveling the underlying mechanisms of reduced amyloidogenic properties in human calcitonin via double mutations

Yu-Pei Chang,  Pei-Chun Pan,  Ling-Hsien Tu, 
  • First Published: 19 March 2024
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Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins

Qian Wang,  Christopher DiForte,  Aleksey Aleshintsev,  Gianna Elci,  Shibani Bhattacharya,  Angelo Bongiorno,  Rupal Gupta, 
  • First Published: 19 March 2024
Open Access

Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations

Alice Grieco,  Sergio Boneta,  José A. Gavira,  Angel L. Pey,  Shibom Basu,  Julien Orlans,  Daniele de Sanctis,  Milagros Medina,  Jose Manuel Martin-Garcia, 
  • First Published: 19 March 2024

RESEARCH NOTE

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Reengineering of a flavin-binding fluorescent protein using ProteinMPNN

Andrey Nikolaev,  Alexander Kuzmin,  Elena Markeeva,  Elizaveta Kuznetsova,  Yury L. Ryzhykau,  Oleg Semenov,  Arina Anuchina,  Alina Remeeva,  Ivan Gushchin, 
  • First Published: 19 March 2024

RESEARCH ARTICLES

Open Access

Disrupted protein interaction dynamics in a genetic neurodevelopmental disorder revealed by structural bioinformatics and genetic code expansion

Valerio Marino,  Wanchana Phromkrasae,  Michele Bertacchi,  Paul Cassini,  Krittalak Chakrabandhu,  Daniele Dell'Orco,  Michèle Studer, 
  • First Published: 21 March 2024
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Ca2+/CaM dependent protein kinase II (CaMKII)α and CaMKIIβ hub domains adopt distinct oligomeric states and stabilities

Can Özden,  Sara MacManus,  Ruth Adafia,  Alfred Samkutty,  Ana P. Torres-Ocampo,  Scott C. Garman,  Margaret M. Stratton, 
  • First Published: 19 March 2024
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Detection of insulin oligomeric forms by a novel surface plasmon resonance-diffusion coefficient based approach

Damiano Calcagno,  Maria Luisa Perina,  Gabriele Antonio Zingale,  Irene Pandino,  Nunzio Tuccitto,  Valentina Oliveri,  Maria Cristina Parravano,  Giuseppe Grasso, 
  • First Published: 19 March 2024

CORRECTION

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Correction to “A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins”

  • First Published: 19 March 2024

RESEARCH ARTICLES

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Mechanosensitive channel MscL gating transitions coupling with constriction point shift

Mingfeng Zhang,  Siyang Tang,  Xiaomin Wang,  Sanhua Fang,  Yuezhou Li, 
  • First Published: 19 March 2024
Open Access

Sensitive detection of SARS-CoV-2 main protease 3CLpro with an engineered ribonuclease zymogen

Evans C. Wralstad,  Ronald T. Raines, 
  • First Published: 19 March 2024
Free Access

Synthesis of site-specific Fab-drug conjugates using ADP-ribosyl cyclases

Hyo Sun Kim,  Kimia Hariri,  Xiao-Nan Zhang,  Liang-Chieh Chen,  Benjamin B. Katz,  Hua Pei,  Stan G. Louie,  Yong Zhang, 
  • First Published: 19 March 2024
Open Access

HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function

Pascaline Bories,  Julie Rima,  Samuel Tranier,  Julien Marcoux,  Yasmina Grimoire,  Mathilde Tomaszczyk,  Anne Launay,  Karine Fata,  Hedia Marrakchi,  Odile Burlet-Schiltz,  Lionel Mourey,  Manuelle Ducoux-Petit,  Fabienne Bardou,  Cécile Bon,  Annaïk Quémard, 
  • First Published: 19 March 2024
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Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance

Lu Zhang,  Wei Dai,  Shuo Rong,  Ulrich Schwaneberg,  Guochao Xu,  Ye Ni, 
  • First Published: 19 March 2024
Free Access

Rational evolution for altering the ligand preference of estrogen receptor alpha

Roy Eerlings,  Purvi Gupta,  Xiao Yin Lee,  Tien Nguyen,  Sarah El Kharraz,  Florian Handle,  Elien Smeets,  Lisa Moris,  Wout Devlies,  Bram Vandewinkel,  Irina Thiry,  Duy Tien Ta,  Anton Gorkovskiy,  Karin Voordeckers,  Els Henckaerts,  Vitor B. Pinheiro,  Frank Claessens,  Kevin J. Verstrepen,  Arnout Voet,  Christine Helsen, 
  • First Published: 21 March 2024
Open Access

Oligomerization mediated by the D2 domain of DTX3L is critical for DTX3L-PARP9 reading function of mono-ADP-ribosylated androgen receptor

Carlos Vela-Rodríguez,  Chunsong Yang,  Heli I. Alanen,  Rebeka Eki,  Tarek A. Abbas,  Mirko M. Maksimainen,  Tuomo Glumoff,  Ramona Duman,  Armin Wagner,  Bryce M. Paschal,  Lari Lehtiö, 
  • First Published: 21 March 2024
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Unraveling paralog-specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors

Kristen M. Ramsey,  Doug Barrick, 
  • First Published: 21 March 2024
Open Access

Proinsulin folding and trafficking defects trigger a common pathological disturbance of endoplasmic reticulum homeostasis

Anoop Arunagiri,  Maroof Alam,  Leena Haataja,  Hassan Draz,  Bashiyer Alasad,  Praveen Samy,  Nadeed Sadique,  Yue Tong,  Ying Cai,  Hadis Shakeri,  Federica Fantuzzi,  Hazem Ibrahim,  Insook Jang,  Vaibhav Sidarala,  Scott A. Soleimanpour,  Leslie S. Satin,  Timo Otonkoski,  Miriam Cnop,  Pamela Itkin-Ansari,  Randal J. Kaufman,  Ming Liu,  Peter Arvan, 
  • First Published: 21 March 2024

METHODS AND APPLICATIONS

Free Access

Efficient and economic protein labeling for NMR in mammalian expression systems: Application to a preT-cell and T-cell receptor protein

Robert J. Mallis,  Jonathan J. Lee,  Arjen Van den Berg,  Kristine N. Brazin,  Thibault Viennet,  Jonathan Zmuda,  Melissa Cross,  Denitsa Radeva,  Ricard Rodriguez-Mias,  Judit Villén,  Vladimir Gelev,  Ellis L. Reinherz,  Haribabu Arthanari, 
  • First Published: 21 March 2024

RESEARCH ARTICLES

Open Access

Copper ion incorporation in α-synuclein amyloids

Gulshan Walke,  Ranjeet Kumar,  Pernilla Wittung-Stafshede, 
  • First Published: 21 March 2024
Free Access

Liquid–liquid phase separation of α-synuclein is highly sensitive to sequence complexity

Anindita Mahapatra,  Robert W. Newberry, 
  • First Published: 21 March 2024
Open Access

DNA-dependent phase separation by human SSB2 (NABP1/OBFC2A) protein points to adaptations to eukaryotic genome repair processes

Zoltán J. Kovács,  Gábor M. Harami,  János Pálinkás,  Natalie Kuljanishvili,  József Hegedüs,  Hajnalka Harami-Papp,  Lamiya Mahmudova,  Lana Khamisi,  Gergely Szakács,  Mihály Kovács, 
  • First Published: 21 March 2024
Open Access

Engineering a monobody specific to monomeric Cu/Zn-superoxide dismutase associated with amyotrophic lateral sclerosis

Hiroshi Amesaka,  Mizuho Hara,  Yuki Sakai,  Atsuko Shintani,  Kaori Sue,  Tomoyuki Yamanaka,  Shun-ichi Tanaka,  Yoshiaki Furukawa, 
  • First Published: 21 March 2024
Open Access

Engineering quorum quenching acylases with improved kinetic and biochemical properties

Kitty Sompiyachoke,  Mikael H. Elias, 
  • First Published: 23 March 2024
Free Access

Inhibitory protein–protein interactions of the SIRT1 deacetylase are choreographed by post-translational modification

Troy C. Krzysiak,  You-Jin Choi,  Yong Joon Kim,  Yunhan Yang,  Christopher DeHaven,  Lariah Thompson,  Ryan Ponticelli,  Mara M. Mermigos,  Laurel Thomas,  Andrea Marquez,  Ian Sipula,  Jongsook Kim Kemper,  Michael Jurczak,  Gary Thomas,  Angela M. Gronenborn, 
  • First Published: 27 March 2024

TOOLS FOR PROTEIN SCIENCE

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MA-PEP: A novel anticancer peptide prediction framework with multimodal feature fusion based on attention mechanism

Xiao Liang,  Haochen Zhao,  Jianxin Wang, 
  • First Published: 27 March 2024
Open Access

KCD: A prediction web server of knowledge-based circular dichroism

Damián Jacinto-Méndez,  Carmen Giovana Granados-Ramírez,  Mauricio D. Carbajal-Tinoco, 
  • First Published: 27 March 2024

REVIEW ARTICLES

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Protein structure–function continuum model: Emerging nexuses between specificity, evolution, and structure

Munishwar Nath Gupta,  Vladimir N. Uversky, 
  • First Published: 27 March 2024

RESEARCH ARTICLES

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Role of UDP-N-acetylmuramic acid in the regulation of MurA activity revealed by molecular dynamics simulations

Maycon Vinicius Damasceno de Oliveira,  Kauê S. da Costa,  José Rogério A. Silva,  Jerônimo Lameira,  Anderson H. Lima, 
  • First Published: 27 March 2024
Open Access

Conserved proline residues prevent dimerization and aggregation in the β-lactamase BlaC

A. Chikunova,  M. P. Manley,  C. N. Heijjer,  C. S. Drenth,  A. J. Cramer-Blok,  M. Ud Din Ahmad,  A. Perrakis,  M. Ubbink, 
  • First Published: 27 March 2024
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Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion

Nika Gladkov,  Elena A. Scott,  Kyle Meador,  Eric J. Lee,  Arthur D. Laganowsky,  Todd O. Yeates,  Roger Castells-Graells, 
  • First Published: 27 March 2024
Open Access

Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding

Ilhan Tomris,  Roosmarijn van der Woude,  Rebeca de Paiva Froes Rocha,  Alba Torrents de la Peña,  Andrew B. Ward,  Robert P. de Vries, 
  • First Published: 27 March 2024

REVIEW ARTICLES

Open Access

Integrating the analysis of human biopsies using post-translational modifications proteomics

Sonali Bhardwaj,  Mitchell Bulluss,  Ana D'Aubeterre,  Afshin Derakhshani,  Regan Penner,  MaryAnn Mahajan,  Vinit B. Mahajan,  Antoine Dufour, 
  • First Published: 27 March 2024