Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

The WEKA data mining software: an update

Hall, M., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., & Witten, I. H. (2009) · ACM SIGKDD Explorations Newsletter · doi:10.1145/1656274.1656278 · Cited by 17,750 · see citing works

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

Arnold, K., Bordoli, L., Kopp, J., & Schwede, T. F. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti770 · Cited by 6,951 · see citing works

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

Carpenter, A. E., Jones, T. R., Lamprecht, M. R., Clarke, C., Kang, I. H., Friman, O., Guertin, D. A., Chang, J. H., Lindquist, R. A., Moffat, J., et al. (2006) · Genome biology · doi:10.1186/gb-2006-7-10-r100 · Cited by 5,077 · see citing works

Molecular chaperones in protein folding and proteostasis

Hartl, F. U., Bracher, A., & Hayer-Hartl, M. K. (2011) · Nature · doi:10.1038/nature10317 · Cited by 3,525 · see citing works

Brownian dynamics with hydrodynamic interactions

Ermak, D., & McCammon, J. (1978) · The Journal of Chemical Physics · doi:10.1063/1.436761 · Cited by 2,238 · see citing works

Cell-free translation reconstituted with purified components

Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., & Ueda, T. (2001) · Nature Biotechnology · doi:10.1038/90802 · Cited by 1,826 · see citing works

The many faces of α-synuclein: from structure and toxicity to therapeutic target

Lashuel, H. A., Overk, C., Oueslati, A., & Masliah, E. (2012) · Nature reviews. Neuroscience · doi:10.1038/nrn3406 · Cited by 1,623 · see citing works

The molecular structure of green fluorescent protein

Yang, F., Moss, L. G., & Phillips, G. N. (1996) · Nature Biotechnology · doi:10.1038/nbt1096-1246 · Cited by 1,580 · see citing works

Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research

Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H., & Mori, H. (2006) · DNA Research · doi:10.1093/dnares/dsi012 · Cited by 1,388 · see citing works

Converging concepts of protein folding in vitro and in vivo

Hartl, F. U., & Hayer-Hartl, M. K. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1591 · Cited by 1,186 · see citing works

Structural Symmetry and Protein Function

Goodsell, D. S., & Olson, A. J. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.105 · Cited by 950 · see citing works

Rapid protein-folding assay using green fluorescent protein

Waldo, G. S., Standish, B. M., Berendzen, J., & Terwilliger, T. C. (1999) · Nature Biotechnology · doi:10.1038/10904 · Cited by 906 · see citing works

Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry

Hernández, H., & Robinson, C. V. (2007) · Nature Protocols · doi:10.1038/nprot.2007.73 · Cited by 655 · see citing works

Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae

Sheff, M. A., & Thorn, K. S. (2004) · Yeast · doi:10.1002/yea.1130 · Cited by 654 · see citing works

DnaK, DnaJ and GrpE form a cellular chaperone machinery capable of repairing heat‐induced protein damage.

Schröder, H., Langer, T., Hartl, F. U., & Bukau, B. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb06097.x · Cited by 605 · see citing works

Crystal Structure of the Tetramerization Domain of the p53 Tumor Suppressor at 1.7 Angstroms

Jeffrey, P. D., Gorina, S. S., & Pavletich, N. P. (1995) · Science · doi:10.1126/science.7878469 · Cited by 548 · see citing works

A Tandem Mass Spectrometer for Improved Transmission and Analysis of Large Macromolecular Assemblies

Sobott, F., Hernández, H., McCammon, M. G., Tito, M. A., & Robinson, C. V. (2002) · Analytical Chemistry · doi:10.1021/ac0110552 · Cited by 511 · see citing works

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

Pechmann, S., & Frydman, J. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2466 · Cited by 487 · see citing works

Structure, Dynamics, Assembly, and Evolution of Protein Complexes

Marsh, J. A., & Teichmann, S. A. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034142 · Cited by 455 · see citing works

Protein folding: local structures, domains, subunits, and assemblies

Jaenicke, R. (1991) · Biochemistry · doi:10.1021/bi00227a001 · Cited by 440 · see citing works

Chromophore Formation in Green Fluorescent Protein

Reid, B. G., & Flynn, G. C. (1997) · Biochemistry · doi:10.1021/bi970281w · Cited by 439 · see citing works

The Determinants of pKas in Proteins

Antosiewicz, J. M., McCammon, J. A., & Gilson, M. K. (1996) · Biochemistry · doi:10.1021/bi9601565 · Cited by 424 · see citing works

Protein synthesis by pure translation systems

Shimizu, Y., Kanamori, T., & Ueda, T. (2005) · Methods · doi:10.1016/j.ymeth.2005.04.006 · Cited by 413 · see citing works

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

Buhr, F., Jha, S., Thommen, M., Mittelstaet, J., Kutz, F., Schwalbe, H., Rodnina, M. V., & Komar, A. A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.01.008 · Cited by 395 · see citing works

DnaK Functions as a Central Hub in the E. coli Chaperone Network

Calloni, G., Chen, T., Schermann, S. M., Chang, H.-C., Genevaux, P., Agostini, F., Tartaglia, G. G., Hayer-Hartl, M. K., & Hartl, F. U. (2012) · Cell Reports · doi:10.1016/j.celrep.2011.12.007 · Cited by 384 · see citing works

Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction

Xiang, Z., Soto, C. S., & Honig, B. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102179699 · Cited by 368 · see citing works

Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of <i>Escherichia coli</i> proteins

Niwa, T., Ying, B.-W., Saito, K., Jin, W., Takada, S., Ueda, T., & Taguchi, H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811922106 · Cited by 321 · see citing works

The importance of sequence diversity in the aggregation and evolution of proteins

Wright, C. F., Teichmann, S. A., Clarke, J., & Dobson, C. M. (2005) · Nature · doi:10.1038/nature04195 · Cited by 315 · see citing works

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

Velankar, S. S., Dana, J. M., Jacobsen, J. O. B., van Ginkel, G., Gane, P. J., Luo, J., Oldfield, T. J., O’Donovan, C., Martin, M. J., & Kleywegt, G. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1258 · Cited by 277 · see citing works

The native 3D organization of bacterial polysomes

Brandt, F., Etchells, S. A., Ortiz, J. O., Elcock, A. H., Hartl, F. U., & Baumeister, W. (2009) · Cell · doi:10.1016/j.cell.2008.11.016 · Cited by 258 · see citing works

Principles of assembly reveal a periodic table of protein complexes

Ahnert, S. E., Marsh, J. A., Hernández, H., Robinson, C. V., & Teichmann, S. A. (2015) · Science · doi:10.1126/science.aaa2245 · Cited by 253 · see citing works

Proteins evolve on the edge of supramolecular self-assembly

Garcia-Seisdedos, H., Empereur-Mot, C., Elad, N., & Levy, E. D. (2017) · Nature · doi:10.1038/nature23320 · Cited by 253 · see citing works

Synonymous Mutations and Ribosome Stalling Can Lead to Altered Folding Pathways and Distinct Minima

Tsai, C., Sauna, Z. E., Kimchi‐Sarfaty, C., Ambudkar, S. V., Gottesman, M. M., & Nussinov, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.08.012 · Cited by 250 · see citing works

Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

Marsh, J. A., Hernández, H., Hall, Z., Ahnert, S. E., Perica, T., Robinson, C. V., & Teichmann, S. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.044 · Cited by 245 · see citing works

The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation

Tam, S. J., Spiess, C., Auyeung, W., Joachimiak, Ł. A., Chen, B., Poirier, M. A., & Frydman, J. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1700 · Cited by 243 · see citing works

CIDRE: an illumination-correction method for optical microscopy

Smith, K., Li, Y., Piccinini, F., Csúcs, G., Balázs, C., Bevilacqua, A., & Horváth, P. (2015) · Nature Methods · doi:10.1038/nmeth.3323 · Cited by 188 · see citing works

Operon structure and cotranslational subunit association direct protein assembly in bacteria

Shieh, Y., Mínguez, P., Peer Bork, B., Auburger, J. J., Guilbride, D. L., Krämer, G., & Bukau, B. (2015) · Science · doi:10.1126/science.aac8171 · Cited by 186 · see citing works

Global analysis of chaperone effects using a reconstituted cell-free translation system

Niwa, T., Kanamori, T., Ueda, T., & Taguchi, H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201380109 · Cited by 184 · see citing works

Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins

Borgia, M. B., Borgia, A., Best, R. B., Steward, A., Nettels, D., Wunderlich, B., Schuler, B., & Clarke, J. (2011) · Nature · doi:10.1038/nature10099 · Cited by 177 · see citing works

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

Levy, E. D., De, S., & Teichmann, S. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1209312109 · Cited by 175 · see citing works

Folding at the birth of the nascent chain: coordinating translation with co-translational folding

Zhang, G., & Ignatova, Z. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.10.008 · Cited by 172 · see citing works

Expanding Anfinsen’s Principle: Contributions of Synonymous Codon Selection to Rational Protein Design

Sander, I. M., Chaney, J. L., & Clark, P. L. (2014) · Journal of the American Chemical Society · doi:10.1021/ja411302m · Cited by 171 · see citing works

Folding and association of oligomeric and multimeric proteins

Jaenicke, R., & Lilie, H. (2000) · Advances in protein chemistry · doi:10.1016/s0065-3233(00)53007-1 · Cited by 157 · see citing works

Nine hydrophobic side chains are key determinants of the thermodynamic stability and oligomerization status of tumour suppressor p53 tetramerization domain

Mateu, M. G., & Fersht, A. R. (1998) · The EMBO Journal · doi:10.1093/emboj/17.10.2748 · Cited by 146 · see citing works

Structural, Evolutionary, and Assembly Principles of Protein Oligomerization

Levy, E. D., & Teichmann, S. A. (2013) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-386931-9.00002-7 · Cited by 143 · see citing works

Biogenesis of p53 Involves Cotranslational Dimerization of Monomers and Posttranslational Dimerization of Dimers

Nicholls, C. D., McLure, K. G., Shields, M. A., & Lee, P. W. K. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m108815200 · Cited by 134 · see citing works

Activation and control of p53 tetramerization in individual living cells

Gaglia, G., Guan, Y., Shah, J. V., & Lahav, G. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1311126110 · Cited by 126 · see citing works

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

Frembgen-Kesner, T., & Elcock, A. H. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct800499p · Cited by 118 · see citing works

PiQSi: Protein Quaternary Structure Investigation

Levy, E. D. (2007) · Structure · doi:10.1016/j.str.2007.09.019 · Cited by 116 · see citing works

Single-Molecule characterization of oligomerization kinetics and equilibria of the tumor suppressor p53

Rajagopalan, S., Huang, F. L., & Fersht, A. R. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq800 · Cited by 110 · see citing works

Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution

Marsh, J. A., & Teichmann, S. A. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001870 · Cited by 104 · see citing works

Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome

Elcock, A. H. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020098 · Cited by 104 · see citing works

Evolution of new protein topologies through multistep gene rearrangements

Peisajovich, S. G., Rockah-Shmuel, L., & Tawfik, D. S. (2006) · Nature Genetics · doi:10.1038/ng1717 · Cited by 102 · see citing works

Characterization of p53 oligomerization domain mutations isolated from Li–Fraumeni and Li–Fraumeni like family members

Lomax, M. E., Barnes, D. M., Hupp, T. R., Picksley, S. M., & Camplejohn, R. (1998) · Oncogene · doi:10.1038/sj.onc.1201974 · Cited by 100 · see citing works

Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity and trapping in the ribosome tunnel

Elcock, A. H. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020098.eor · Cited by 99 · see citing works

Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53.

Fersht, A. R., Mateu, M. G., & del Pino, M. M. S. (1999) · Nature Structural Biology · doi:10.1038/5880 · Cited by 98 · see citing works

Interaction of the p53 DNA-Binding Domain with Its N-Terminal Extension Modulates the Stability of the p53 Tetramer

Natan, E., Baloğlu, Ç., Pagel, K., Freund, S. M. V., Morgner, N., Robinson, C. V., Fersht, A. R., & Joerger, A. C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.03.047 · Cited by 98 · see citing works

Futile Protein Folding Cycles in the ER Are Terminated by the Unfolded Protein O-Mannosylation Pathway

Xu, C., Wang, S., Thibault, G., & Ng, D. (2013) · Science · doi:10.1126/science.1234055 · Cited by 97 · see citing works

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

Ruff, K. M., Harmon, T. S., & Pappu, R. V. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4935066 · Cited by 93 · see citing works

Prediction of variable translation rate effects on cotranslational protein folding

O’Brien, E. P., Vendruscolo, M., & Dobson, C. M. (2012) · Nature Communications · doi:10.1038/ncomms1850 · Cited by 91 · see citing works

Protein Folding Requires Crowd Control in a Simulated Cell

Jefferys, B. R., Kelley, L. A., & Sternberg, M. J. E. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.01.074 · Cited by 89 · see citing works

Conformational Flexibility and Folding of Synthetic Peptides Representing an Interdomain Segment of Polypeptide Chain in the Pyruvate Dehydrogenase Multienzyme Complex of Escherichia coli

Radford, S. E., Laue, E. D., Perham, R. N., Martin, S. R., & Appella, E. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)85008-1 · Cited by 81 · see citing works

Cotranslational Folding Increases GFP Folding Yield

Ugrinov, K. G., & Clark, P. L. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2009.12.4291 · Cited by 76 · see citing works

Regulation, evolution and consequences of cotranslational protein complex assembly

Natan, E., Wells, J. N., Teichmann, S. A., & Marsh, J. A. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.11.023 · Cited by 75 · see citing works

Mutually compensatory mutations during evolution of the tetramerization domain of tumor suppressor p53 lead to impaired hetero-oligomerization

Mateu, M. G., & Fersht, A. R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.7.3595 · Cited by 74 · see citing works

Trigger Factor Slows Co-translational Folding through Kinetic Trapping while Sterically Protecting the Nascent Chain from Aberrant Cytosolic Interactions

O’Brien, E. P., Christodoulou, J. C., Vendruscolo, M., & Dobson, C. M. (2012) · Journal of the American Chemical Society · doi:10.1021/ja302305u · Cited by 74 · see citing works

Restricted Motion of the Lipoyl-Lysine Swinging Arm in the Pyruvate Dehydrogenase Complex of Escherichia coli,

Jones, D. D., Stott, K. M., Howard, M. J., & Perham, R. N. (2000) · Biochemistry · doi:10.1021/bi992978i · Cited by 58 · see citing works

Structural insights into cognate versus near‐cognate discrimination during decoding

Agirrezabala, X., Schreiner, E., Trabuco, L. G., Lei, J., Ortiz‐Meoz, R. F., Schulten, K. J., Green, R., & Frank, J. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.58 · Cited by 56 · see citing works

Structural and evolutionary versatility in protein complexes with uneven stoichiometry

Marsh, J. A., Rees, H. A., Ahnert, S. E., & Teichmann, S. A. (2015) · Nature Communications · doi:10.1038/ncomms7394 · Cited by 50 · see citing works

Timing Is Everything: Unifying Codon Translation Rates and Nascent Proteome Behavior

Nissley, D. A., & O’Brien, E. P. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510082j · Cited by 44 · see citing works

Studies on Bacterial Inclusion Bodies

de Groot, N. S., Espargaró, A., Morell, M., & Ventura, S. (2008) · Future Microbiology · doi:10.2217/17460913.3.4.423 · Cited by 41 · see citing works

Co-translational assembly of protein complexes

Wells, J. N., Bergendahl, L. T., & Marsh, J. A. (2015) · Biochemical Society Transactions · doi:10.1042/bst20150159 · Cited by 38 · see citing works

Structure and Kinetic Stability of the p63 Tetramerization Domain

Natan, E., & Joerger, A. C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.11.007 · Cited by 35 · see citing works

Extended Polypeptide Linkers Establish the Spatial Architecture of a Pyruvate Dehydrogenase Multienzyme Complex

Lengyel, J. S., Stott, K. M., Wu, X., Brooks, B. R., Balbo, A., Schuck, P., Perham, R. N., Subramaniam, S., & Milne, J. L. S. (2008) · Structure · doi:10.1016/j.str.2007.10.017 · Cited by 25 · see citing works

Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions

Winter, U., & Geyer, T. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3216573 · Cited by 22 · see citing works

Seeing translation

Iwasaki, S., & Ingolia, N. T. (2016) · Science · doi:10.1126/science.aag1039 · Cited by 21 · see citing works

A DAG-based parallel Cholesky factorization for multicore systems

Hogg, J. D. (2008) · Science and Technology Facilities Council · doi:10.5286/raltr.2008029 · Cited by 11 · see citing works

Mechanisms of Cotranslational Maturation of Newly Synthesized Proteins

Krämer, G., Shiber, A., & Bukau, B. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-111717 · Cited by 186 · see citing works

Interactions between nascent proteins translated by adjacent ribosomes drive homomer assembly

Bertolini, M., Fenzl, K., Kats, I., Wruck, F., Tippmann, F., Schmitt, J. L., Auburger, J. J., Tans, S. J., Bukau, B., & Krämer, G. (2020) · Science · doi:10.1126/science.abc7151 · Cited by 153 · see citing works

Co-translational assembly of mammalian nuclear multisubunit complexes

Kamenova, I., Mukherjee, P., Conic, S., Mueller, F., El-Saafin, F., Bardot, P., Garnier, J., Dembélé, D., Capponi, S., Timmers, H. T. M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09749-y · Cited by 120 · see citing works

Solubility-Weighted Index: fast and accurate prediction of protein solubility

Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa578 · Cited by 97 · see citing works

Designer protein assemblies with tunable phase diagrams in living cells

Heidenreich, M., Georgeson, J. M., Locatelli, E., Rovigatti, L., Nandi, S. K., Steinberg, A., Nadav, Y., Shimoni, E., Safran, S. A., Doye, J. P. K., et al. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0576-z · Cited by 99 · see citing works

The Benefits of Cotranslational Assembly: A Structural Perspective

Schwarz, A., & Beck, M. (2019) · Trends in Cell Biology · doi:10.1016/j.tcb.2019.07.006 · Cited by 72 · see citing works

Regulation, evolution and consequences of cotranslational protein complex assembly

Natan, E., Wells, J. N., Teichmann, S. A., & Marsh, J. A. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.11.023 · Cited by 75 · see citing works

The Effects of Codon Usage on Protein Structure and Folding

Moss, M. J., Chamness, L. M., & Clark, P. L. (2023) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-030722-020555 · Cited by 64 · see citing works

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Bitran, A., Jacobs, W. M., Zhai, X., & Shakhnovich, E. I. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1913207117 · Cited by 57 · see citing works

Co-translational assembly orchestrates competing biogenesis pathways

Seidel, M., Becker, A., Pereira, F. M., Landry, J. J. M., de Azevedo, N. T. D., Fusco, C. M., Kaindl, E., Romanov, N., Baumbach, J., Langer, J. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28878-5 · Cited by 52 · see citing works

Structural determinants of co-translational protein complex assembly

Mallik, S., Venezian, J., Lobov, A., Heidenreich, M., Garcia-Seisdedos, H., Yeates, T. O., Shiber, A., & Levy, E. D. (2025) · Cell · doi:10.1016/j.cell.2024.11.013 · Cited by 42 · see citing works

The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs

Marchant, A., Cisneros, A. F., Dubé, A. K., Gagnon‐Arsenault, I., Ascencio, D., Jain, H., Aubé, S., Eberlein, C., Evans-Yamamoto, D., Yachie, N., et al. (2019) · eLife · doi:10.7554/elife.46754 · Cited by 42 · see citing works

Large protein complex interfaces have evolved to promote cotranslational assembly

Badonyi, M., & Marsh, J. A. (2022) · eLife · doi:10.7554/elife.79602 · Cited by 29 · see citing works

Leveraging protein structural information to improve variant effect prediction

Gerasimavicius, L., Teichmann, S. A., & Marsh, J. A. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103023 · Cited by 32 · see citing works

Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”

Sugimoto, N., Endoh, T., Takahashi, S., & Tateishi-Karimata, H. (2021) · Bulletin of the Chemical Society of Japan · doi:10.1246/bcsj.20210131 · Cited by 19 · see citing works

Protein structure and aggregation: a marriage of necessity ruled by aggregation gatekeepers

Houben, B., Rousseau, F., & Schymkowitz, J. W. H. (2021) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2021.08.010 · Cited by 27 · see citing works

Buffering of genetic dominance by allele-specific protein complex assembly

Badonyi, M., & Marsh, J. A. (2023) · Science Advances · doi:10.1126/sciadv.adf9845 · Cited by 24 · see citing works

A Short Tale of the Origin of Proteins and Ribosome Evolution

Farías‐Rico, J. A., & Mourra-Díaz, C. M. (2022) · Microorganisms · doi:10.3390/microorganisms10112115 · Cited by 21 · see citing works

Co-translational Assembly Pathways of Nuclear Multiprotein Complexes Involved in the Regulation of Gene Transcription

Bernardini, A., & Tora, L. (2023) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168382 · Cited by 15 · see citing works

Puzzling out nuclear pore complex assembly

Penzo, A., & Palancade, B. (2023) · FEBS Letters · doi:10.1002/1873-3468.14713 · Cited by 22 · see citing works

Evolutionary causes and consequences of gene duplication

Cisneros, A. F., Dibyachintan, S., Bédard, F., Aubé, S., Lemieux, P., & Landry, C. R. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00935-5 · Cited by 16 · see citing works

Translation efficiency covariation identifies conserved coordination patterns across cell types

Liu, Y., Rao, S., Hoskins, I., Geng, M., Zhao, Q., Chacko, J., Ghatpande, V., Qi, K., Persyn, L., Wang, J., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02718-5 · Cited by 15 · see citing works

Enzyme symphony in bio-inspired multi-enzyme cascades for enhanced biosynthesis

Liu, H., Wu, L., Zhao, S., Xu, Y., & Nie, Y. (2025) · Biotechnology Advances · doi:10.1016/j.biotechadv.2025.108789 · Cited by 14 · see citing works

Proteome-wide landscape of solubility limits in a bacterial cell

Györkei, Á., Daruka, L., Balogh, D., Őszi, E., Magyar, Z., Szappanos, B., Fekete, G., Fuxreiter, M., Horváth, P., Pál, C., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-10427-1 · Cited by 14 · see citing works

Co-translational ribosome pairing enables native assembly of misfolding-prone subunits

Wruck, F., Schmitt, J. L., Till, K., Fenzl, K., Bertolini, M., Tippmann, F., Katranidis, A., Bukau, B., Krämer, G., & Tans, S. J. (2025) · Nature Communications · doi:10.1038/s41467-025-61500-y · Cited by 13 · see citing works

Native Fold Delay and its implications for co-translational chaperone binding and protein aggregation

Duran-Romaña, R., Houben, B., Migens, P. F., Zhang, Y., Rousseau, F., & Schymkowitz, J. (2025) · Nature Communications · doi:10.1038/s41467-025-57033-z · Cited by 10 · see citing works

Cellular location shapes quaternary structure of enzymes

Abrusán, G., & Zelezniak, A. (2024) · Nature Communications · doi:10.1038/s41467-024-52662-2 · Cited by 9 · see citing works

Volumetric Strategy for Quantitatively Elucidating a Local Hydration Network around a G-Quadruplex

Matsumoto, S., Takahashi, S., Bhowmik, S., Ohyama, T., & Sugimoto, N. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c01075 · Cited by 9 · see citing works

Orientationally Averaged Version of the Rotne–Prager–Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules

Tworek, J. W., & Elcock, A. H. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00476 · Cited by 8 · see citing works

Codon Selection Affects Recruitment of Ribosome-Associating Factors during Translation

Rojano-Nisimura, A. M., Haning, K., Janovsky, J., Vasquez, K. A., Thompson, J. P., & Contreras, L. M. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00344 · Cited by 7 · see citing works

Riboexp: an interpretable reinforcement learning framework for ribosome density modeling

Hu, H., Liu, X., Xiao, A., Li, Y., Zhang, C., Jiang, T., Zhao, D. Y., Song, S., & Zeng, J. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa412 · Cited by 7 · see citing works

Hallmarks and evolutionary drivers of cotranslational protein complex assembly

Badonyi, M., & Marsh, J. A. (2023) · FEBS Journal · doi:10.1111/febs.16869 · Cited by 7 · see citing works

Heterodimer Formation of the Homodimeric ABC Transporter OpuA

Sieiro, P. Á., Sikkema, H. R., & Poolman, B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115912 · Cited by 7 · see citing works

Evolution of interface binding strengths in simplified model of protein quaternary structure

Leonard, A. S., & Ahnert, S. E. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006886 · Cited by 7 · see citing works

Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes

Abrusán, G., & Marsh, J. A. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.014 · Cited by 7 · see citing works

The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis

Roeselová, A., Shivakumaraswamy, S., Jurkeviciute, G., He, J. Z., Auburger, J. J., Schmitt, J. L., Kramer, G., Bukau, B., Enchev, R. I., & Balchin, D. (2026) · Molecular Cell · doi:10.1016/j.molcel.2025.12.022 · Cited by 6 · see citing works

Perturbation of multiprotein complexes in skeletal muscle induces protective proteases in the CNS that degrade pathogenic proteins

Rai, M., Baddeley, H. J. E., Chuang, C.-L., Platt, A., Curley, M., Finkelstein, D., & Demontis, F. (2025) · npj Aging · doi:10.1038/s41514-025-00288-z · Cited by 5 · see citing works

Co-translational assembly counteracts promiscuous interactionsPreprint

Seidel, M., Becker, A., Pereira, F. M., Landry, J. J. M., de Azevedo, N. T. D., Fusco, C. M., Kaindl, E., Baumbach, J., Langer, J. D., Schuman, E. M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.13.452229 · Cited by 4 · see citing works

Condition-dependent amorphous protein agglomerates control cytoplasmic rheology

Losa, J., Simon, F., Linnik, D., Kaya, S., Stuart, M. C. A., Stetsenko, A., de Boer, R., Ho, F. Y., Incarnato, D., Stevens, J. A., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.018 · Cited by 3 · see citing works

N‐terminal domain of ARF‐GEF GNOM prevents heterodimerization with functionally divergent GNL1 in Arabidopsis

Brumm, S., Singh, M. K., Kriechbaum, C., Richter, S., Huhn, K., Kucera, T., Baumann, S., Wolters, H., Takada, S., & Jürgens, G. (2022) · The Plant Journal · doi:10.1111/tpj.15979 · Cited by 3 · see citing works

Born to Condense: Polysomes Drive Co-Translational Condensation of Biomolecular Condensate ProteinsPreprint

He, Z., Chow, C. F. W., Tóth-Petróczy, Á., Sommer, J., & Harmon, T. S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.30.679637 · Cited by 3 · see citing works

Buffering of genetic dominance by allele-specific protein complex assemblyPreprint

Badonyi, M., & Marsh, J. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.17.516863 · Cited by 2 · see citing works

The regulatory subunit of acetohydroxyacid synthase enhances the catalysis of its catalytic subunit on 2-ketobutyrate

Zheng, Z., Wei, Z.-T., Jin, S.-B., Yao, Z., Ma, C.-X., Gao, W., & Li, H. (2026) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2026.110818 · Cited by 1 · see citing works

The twisted tale of cotranslational protein complex assembly

Mallik, S., & Shiber, A. (2026) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2026.103281 · Cited by 1 · see citing works

Assembly in action: Protein structure orchestrates assembly pathway, and intertwining defines co-translational assembly

Collart, M. A., & Panasenko, O. O. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.01.007 · Cited by 1 · see citing works

Rationalizing Translation Elongation by Reinforcement LearningPreprint

Hu, H., Liu, X., Xiao, A., Li, Y., Zhang, C., Jiang, T., Zhao, D., Song, S., & Zeng, J. (2020) · SSRN Electronic Journal · doi:10.2139/ssrn.3543842

Interface size drives cotranslational assembly of protein complexes

Badonyi, M., & Marsh, J. A. (2021) · University of Edinburgh · doi:10.7488/ds/3134

Heterodimers of functionally divergent ARF-GEF paralogues prevented by self-interacting dimerisation domainPreprint

Brumm, S., Singh, M. K., Beckmann, H., Richter, S., Huhn, K., Kucera, T., Baumann, S., Kriechbaum, C., Wolters, H., Takada, S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.14.460214

Dynamic Regulation of Biosystems by Nucleic Acids with Non‐canonical Structures

Sugimoto, N. (2021) · doi:10.1002/9783527817856.ch10

Large protein complex interfaces have evolved to promote cotranslational assemblyPreprint

Badonyi, M., & Marsh, J. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.26.445863

Az Arabidopsis E2FB transzkripciós faktor funkcionális jellemzése

Őszi, E. (2021) · doi:10.14232/phd.10705

AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes

(2024) · doi:10.1016/j.str.2024.02.002

Multimerization

Lynch, M. (2024) · doi:10.1093/oso/9780192847287.003.0013

Co-translational complex assembly

Venezian, J., & Shiber, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-99507-8.00023-8

Histone fold domain positioning dictates cotranslational heterodimeric assembly of paralogous TAF12/TAF12L in Candida albicans

Bhardwaj, V., Swanson, S. K., Florens, L. A., Washburn, M. P., Workman, J. L., & Natarajan, K. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.111239

Cotranslational Assembly of Oligomeric Proteins

Santos, J., Tans, S. J., Ban, N., Kramer, G., & Bukau, B. (2026) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051024-124747 · Cited by 2 · see citing works

Study of the co-translational assembly mechanism of transcription complexes in mammalian cells

Mukherjee, P. (2019) · theses.fr (ABES) · doi:10.70675/738c094cz1dc9z431fzaf17zad0fb9e6be1c

Born to Condense: Polysomes Drive Cotranslational Condensation of Biomolecular Condensate Proteins

He, Z., Chow, C. F. W., Tóth-Petróczy, Á., Sommer, J., & Harmon, T. S. (2026) · PRX Life · doi:10.1103/gjtk-ddjr

Cotranslational protein assembly imposes \nevolutionary constraints on homomeric proteins

Eviatar, N., Tamaki, E., Haim-Vilmovsky, L., Kintses, B., Horváth, P., Fekete, G., Pál, C., Papp, B., Őszi, E., & Magyar, Z. (2018) · Repository of the Academy's Library (Library of the Hungarian Academy of Sciences)

Testing mechanisms for homomeric protein assembly in vivo

Moss, M. J., & Clark, P. L. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2022.11.2502

Hallmarks and evolutionary drivers of cotranslational protein complex assembly

Badonyi, M., & Marsh, J. A. (2023) · FEBS Journal · doi:10.1111/febs.16869 · Cited by 7 · see citing works

Cotranslational Assembly of Oligomeric Proteins

Santos, J., Tans, S. J., Ban, N., Krämer, G., & Bukau, B. (2026) · Repository for Publications and Research Data (ETH Zurich) · doi:10.3929/ethz-c-000802698

Large protein complex interfaces have evolved to promote cotranslational assemblyPreprint

Badonyi, M., & Marsh, J. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.26.445863