Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling

Following endocytosis into the endosomal network, integral membrane proteins undergo sorting for lysosomal degradation or are retrieved and recycled back to the cell surface. Here we describe the discovery of an ancient and conserved multiprotein complex that orchestrates cargo retrieval and recycling and, importantly, is biochemically and functionally distinct from the established retromer pathway. We have called this complex 'retriever'; it is a heterotrimer composed of DSCR3, C16orf62 and VPS29, and bears striking similarity to retromer. We establish that retriever associates with the cargo adaptor sorting nexin 17 (SNX17) and couples to CCC (CCDC93, CCDC22, COMMD) and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of α5β1 integrin. Through quantitative proteomic analysis, we identify over 120 cell surface proteins, including numerous integrins, signalling receptors and solute transporters, that require SNX17-retriever to maintain their surface levels. Our\ua0identification of retriever establishes a major endosomal retrieval and recycling pathway

De novo design of modular peptide-binding proteins by superhelical matching.

Acknowledgements: We thank B. Wicky, A. Ljubetic and I. Lutz for advice on the split luciferase assay for the second-round design screening; C. Xu for help troubleshooting experiments; T. Schlichtharle for discussion; L. Cao for advice on bio-layer interferometry; H. Pyles for advice on circular dichroism and DHR proteins; R. Hegde for the suggestion to target disordered regions of endogenous proteins; and K. Van Wormer and A. Curtis Smith for laboratory support during COVID-19. This work was supported by the Audacious Project at the Institute for Protein Design (D.B., K.W., M.D., D.A.S. and A.B.); the Michelson Found Animals Foundation grant number GM15-S01 (L.S., K.W. and D.B.); the National Institute on Aging grant 5U19AG065156-02 (D.R.H., K.W. and D.B.); the National Institute of General Medical Sciences grant R35GM128777 (D.C.E.); the Howard Hughes Medical Institute (D.B., W.S. and H.B.); the Open Philanthropy Project Improving Protein Design Fund (Y.-T.C., R.R., C.M.C., G.B., D.C.E. and D.B.); the Donald and Jo Anne Petersen Endowment for Accelerating Advancements in Alzheimer’s Disease Research (T.J.B. and D.B.); a donation from AMGEN to the Institute for Protein Design (I.G.); the Medical Research Council (MC_UP_1201/13 to E.D., T.E.M. and T.J.S.); the Human Frontier Science Program (CDA00034/2017-C to E.D.); and a Sir Henry Wellcome Postdoctoral Fellowship (220480/Z/20/Z to K.E.M.).General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in isolation, and hydrogen bonds must be made to the buried polar groups in the peptide backbone1-3. Here, inspired by natural and re-engineered protein-peptide systems4-11, we set out to design proteins made out of repeating units that bind peptides with repeating sequences, with a one-to-one correspondence between the repeat units of the protein and those of the peptide. We use geometric hashing to identify protein backbones and peptide-docking arrangements that are compatible with bidentate hydrogen bonds between the side chains of the protein and the peptide backbone12. The remainder of the protein sequence is then optimized for folding and peptide binding. We design repeat proteins to bind to six different tripeptide-repeat sequences in polyproline II conformations. The proteins are hyperstable and bind to four to six tandem repeats of their tripeptide targets with nanomolar to picomolar affinities in vitro and in living cells. Crystal structures reveal repeating interactions between protein and peptide interactions as designed, including ladders of hydrogen bonds from protein side chains to peptide backbones. By redesigning the binding interfaces of individual repeat units, specificity can be achieved for non-repeating peptide sequences and for disordered regions of native proteins

Macromolecular condensation buffers intracellular water potential

Acknowledgements: The order of the second and corresponding authors is arbitrary and these authors can change the order of their respective names to suit their own interests. This work has been supported by the Medical Research Council, as part of United Kingdom Research and Innovation (MC_UP_1201/13 to E.D.; MC_UP_1201/4 to J.S.O. and MCMB MR/V028669/1 to J.E.C.), the Human Frontier Science Program (Career Development Award CDA00034/2017 to E.D.), a Versus Arthritis Senior Research Fellowship Award (20875 to Q.-J.M.) and an MRC project grant (MR/K019392/1 to Q.-J.M.), a Grifols ‘ALTA’ Alpha-1-Antitrypsin Laurell’s Training Award and an Alpha-1-Foundation (grant number 614939) to J.E.C., and by a Wellcome Trust Sir Henry Dale Fellowship (208790/Z/17/Z to R.S.E.). N.M.R. is supported by a Medical Research Council Clinician Scientist Fellowship (MR/S022023/1). L.K.K. and V.J.P.-H. are recipients of EMBO Postdoctoral fellowships (ALTF 876-2021 and ALTF 577-2018, respectively). K.E.M. is supported by the Wellcome Trust through a Sir Henry Wellcome Postdoctoral Fellowship (220480/Z/20/Z). P.M.M. and J.B. were supported by Volkswagen ‘Life’ grant number 96827 and the DFG Excellence Cluster Physics of Life. We thank H. Andreas for frog maintenance; C. Godlee and M. Kaksonen for the gift of unpublished S. cerevisiae yeast strains and initial discussion of yeast experiments about temperature; P. Tran for S. pombe yeast strains; L. Miller for help with yeast work; A. Bertolotti for the kind gift of SH-SY5Y cells; and C. Russo, F. Jülicher, M. Gonzalez-Gaitan, K. Kruse, L. Blanchoin, J. Löwe, R. Hegde, P. Farrell and P. Crosby for discussion and suggestions; the staff at the companies Cherry Biotech and Elvesys, in particular T. Guérinier, for their help in designing and assembling the custom microfluidics system required for this project; the members of the Electronics and Mechanical workshops of the LMB for key support; the staff at the LMB Mass Spectrometry facility for performing and analysing MS data; and A. Prasad and T. Stevens for sharing the scripts for protein disorder and kinase motif predictions, respectively. Cartoons were created using BioRender. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of ‘structured’ water molecules within their hydration layers, reducing the available ‘free’ bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2, 3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function

Macromolecular condensation buffers intracellular water potential

Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of 'structured' water molecules within their hydration layers, reducing the available 'free' bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2,3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function.</p

Macromolecular condensation buffers intracellular water potential.

Acknowledgements: The order of the second and corresponding authors is arbitrary and these authors can change the order of their respective names to suit their own interests. This work has been supported by the Medical Research Council, as part of United Kingdom Research and Innovation (MC_UP_1201/13 to E.D.; MC_UP_1201/4 to J.S.O. and MCMB MR/V028669/1 to J.E.C.), the Human Frontier Science Program (Career Development Award CDA00034/2017 to E.D.), a Versus Arthritis Senior Research Fellowship Award (20875 to Q.-J.M.) and an MRC project grant (MR/K019392/1 to Q.-J.M.), a Grifols ‘ALTA’ Alpha-1-Antitrypsin Laurell’s Training Award and an Alpha-1-Foundation (grant number 614939) to J.E.C., and by a Wellcome Trust Sir Henry Dale Fellowship (208790/Z/17/Z to R.S.E.). N.M.R. is supported by a Medical Research Council Clinician Scientist Fellowship (MR/S022023/1). L.K.K. and V.J.P.-H. are recipients of EMBO Postdoctoral fellowships (ALTF 876-2021 and ALTF 577-2018, respectively). K.E.M. is supported by the Wellcome Trust through a Sir Henry Wellcome Postdoctoral Fellowship (220480/Z/20/Z). P.M.M. and J.B. were supported by Volkswagen ‘Life’ grant number 96827 and the DFG Excellence Cluster Physics of Life. We thank H. Andreas for frog maintenance; C. Godlee and M. Kaksonen for the gift of unpublished S. cerevisiae yeast strains and initial discussion of yeast experiments about temperature; P. Tran for S. pombe yeast strains; L. Miller for help with yeast work; A. Bertolotti for the kind gift of SH-SY5Y cells; and C. Russo, F. Jülicher, M. Gonzalez-Gaitan, K. Kruse, L. Blanchoin, J. Löwe, R. Hegde, P. Farrell and P. Crosby for discussion and suggestions; the staff at the companies Cherry Biotech and Elvesys, in particular T. Guérinier, for their help in designing and assembling the custom microfluidics system required for this project; the members of the Electronics and Mechanical workshops of the LMB for key support; the staff at the LMB Mass Spectrometry facility for performing and analysing MS data; and A. Prasad and T. Stevens for sharing the scripts for protein disorder and kinase motif predictions, respectively. Cartoons were created using BioRender. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of 'structured' water molecules within their hydration layers, reducing the available 'free' bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2,3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function

Macromolecular condensation buffers intracellular water potential

Acknowledgements: The order of the second and corresponding authors is arbitrary and these authors can change the order of their respective names to suit their own interests. This work has been supported by the Medical Research Council, as part of United Kingdom Research and Innovation (MC_UP_1201/13 to E.D.; MC_UP_1201/4 to J.S.O. and MCMB MR/V028669/1 to J.E.C.), the Human Frontier Science Program (Career Development Award CDA00034/2017 to E.D.), a Versus Arthritis Senior Research Fellowship Award (20875 to Q.-J.M.) and an MRC project grant (MR/K019392/1 to Q.-J.M.), a Grifols ‘ALTA’ Alpha-1-Antitrypsin Laurell’s Training Award and an Alpha-1-Foundation (grant number 614939) to J.E.C., and by a Wellcome Trust Sir Henry Dale Fellowship (208790/Z/17/Z to R.S.E.). N.M.R. is supported by a Medical Research Council Clinician Scientist Fellowship (MR/S022023/1). L.K.K. and V.J.P.-H. are recipients of EMBO Postdoctoral fellowships (ALTF 876-2021 and ALTF 577-2018, respectively). K.E.M. is supported by the Wellcome Trust through a Sir Henry Wellcome Postdoctoral Fellowship (220480/Z/20/Z). P.M.M. and J.B. were supported by Volkswagen ‘Life’ grant number 96827 and the DFG Excellence Cluster Physics of Life. We thank H. Andreas for frog maintenance; C. Godlee and M. Kaksonen for the gift of unpublished S. cerevisiae yeast strains and initial discussion of yeast experiments about temperature; P. Tran for S. pombe yeast strains; L. Miller for help with yeast work; A. Bertolotti for the kind gift of SH-SY5Y cells; and C. Russo, F. Jülicher, M. Gonzalez-Gaitan, K. Kruse, L. Blanchoin, J. Löwe, R. Hegde, P. Farrell and P. Crosby for discussion and suggestions; the staff at the companies Cherry Biotech and Elvesys, in particular T. Guérinier, for their help in designing and assembling the custom microfluidics system required for this project; the members of the Electronics and Mechanical workshops of the LMB for key support; the staff at the LMB Mass Spectrometry facility for performing and analysing MS data; and A. Prasad and T. Stevens for sharing the scripts for protein disorder and kinase motif predictions, respectively. Cartoons were created using BioRender. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of ‘structured’ water molecules within their hydration layers, reducing the available ‘free’ bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2, 3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function

Macromolecular condensation buffers intracellular water potential

Acknowledgements: The order of the second and corresponding authors is arbitrary and these authors can change the order of their respective names to suit their own interests. This work has been supported by the Medical Research Council, as part of United Kingdom Research and Innovation (MC_UP_1201/13 to E.D.; MC_UP_1201/4 to J.S.O. and MCMB MR/V028669/1 to J.E.C.), the Human Frontier Science Program (Career Development Award CDA00034/2017 to E.D.), a Versus Arthritis Senior Research Fellowship Award (20875 to Q.-J.M.) and an MRC project grant (MR/K019392/1 to Q.-J.M.), a Grifols ‘ALTA’ Alpha-1-Antitrypsin Laurell’s Training Award and an Alpha-1-Foundation (grant number 614939) to J.E.C., and by a Wellcome Trust Sir Henry Dale Fellowship (208790/Z/17/Z to R.S.E.). N.M.R. is supported by a Medical Research Council Clinician Scientist Fellowship (MR/S022023/1). L.K.K. and V.J.P.-H. are recipients of EMBO Postdoctoral fellowships (ALTF 876-2021 and ALTF 577-2018, respectively). K.E.M. is supported by the Wellcome Trust through a Sir Henry Wellcome Postdoctoral Fellowship (220480/Z/20/Z). P.M.M. and J.B. were supported by Volkswagen ‘Life’ grant number 96827 and the DFG Excellence Cluster Physics of Life. We thank H. Andreas for frog maintenance; C. Godlee and M. Kaksonen for the gift of unpublished S. cerevisiae yeast strains and initial discussion of yeast experiments about temperature; P. Tran for S. pombe yeast strains; L. Miller for help with yeast work; A. Bertolotti for the kind gift of SH-SY5Y cells; and C. Russo, F. Jülicher, M. Gonzalez-Gaitan, K. Kruse, L. Blanchoin, J. Löwe, R. Hegde, P. Farrell and P. Crosby for discussion and suggestions; the staff at the companies Cherry Biotech and Elvesys, in particular T. Guérinier, for their help in designing and assembling the custom microfluidics system required for this project; the members of the Electronics and Mechanical workshops of the LMB for key support; the staff at the LMB Mass Spectrometry facility for performing and analysing MS data; and A. Prasad and T. Stevens for sharing the scripts for protein disorder and kinase motif predictions, respectively. Cartoons were created using BioRender. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of ‘structured’ water molecules within their hydration layers, reducing the available ‘free’ bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2, 3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function