1
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Korkola NC, Stillman MJ. Human apo-metallothionein 1a is not a random coil: Evidence from guanidinium chloride, high temperature, and acidic pH unfolding studies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141010. [PMID: 38490456 DOI: 10.1016/j.bbapap.2024.141010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
The structures of apo-metallothioneins (apo-MTs) have been relatively elusive due to their fluxional, disordered state which has been difficult to characterize. However, intrinsically disordered protein (IDP) structures are rather diverse, which raises questions about where the structure of apo-MTs fit into the protein structural spectrum. In this paper, the unfolding transitions of apo-MT1a are discussed with respect to the effect of the chemical denaturant GdmCl, temperature conditions, and pH environment. Cysteine modification in combination with electrospray ionization mass spectrometry was used to probe the unfolding transition of apo-MT1a in terms of cysteine exposure. Circular dichroism spectroscopy was also used to monitor the change in secondary structure as a function of GdmCl concentration. For both of these techniques, cooperative unfolding was observed, suggesting that apo-MT1a is not a random coil. More GdmCl was required to unfold the protein backbone than to expose the cysteines, indicating that cysteine exposure is likely an early step in the unfolding of apo-MT1a. MD simulations complement the experimental results, suggesting that apo-MT1a adopts a more compact structure than expected for a random coil. Overall, these results provide further insight into the intrinsically disordered structure of apo-MT.
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Affiliation(s)
- Natalie C Korkola
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada.
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2
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Asakereh I, Rutbeek NR, Singh M, Davidson D, Prehna G, Khajehpour M. The Streptococcus phage protein paratox is an intrinsically disordered protein. Protein Sci 2024; 33:e5037. [PMID: 38801244 PMCID: PMC11129628 DOI: 10.1002/pro.5037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
The bacteriophage protein paratox (Prx) blocks quorum sensing in its streptococcal host by directly binding the signal receptor and transcription factor ComR. This reduces the ability of Streptococcus to uptake environmental DNA and protects phage DNA from damage by recombination. Past work characterizing the Prx:ComR molecular interaction revealed that paratox adopts a well-ordered globular fold when bound to ComR. However, solution-state biophysical measurements suggested that Prx may be conformationally dynamic. To address this discrepancy, we investigated the stability and dynamic properties of Prx in solution using circular dichroism, nuclear magnetic resonance, and several fluorescence-based protein folding assays. Our work shows that under dilute buffer conditions Prx is intrinsically disordered. We also show that the addition of kosmotropic salts or protein stabilizing osmolytes induces Prx folding. However, the solute stabilized fold is different from the conformation Prx adopts when it is bound to ComR. Furthermore, we have characterized Prx folding thermodynamics and folding kinetics through steady-state fluorescence and stopped flow kinetic measurements. Our results show that Prx is a highly dynamic protein in dilute solution, folding and refolding within the 10 ms timescale. Overall, our results demonstrate that the streptococcal phage protein Prx is an intrinsically disordered protein in a two-state equilibrium with a solute-stabilized folded form. Furthermore, the solute-stabilized fold is likely the predominant form of Prx in a solute-crowded bacterial cell. Finally, our work suggests that Prx binds and inhibits ComR, and thus quorum sensing in Streptococcus, by a combination of conformational selection and induced-fit binding mechanisms.
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Affiliation(s)
- Iman Asakereh
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Nicole R. Rutbeek
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
| | - Manvir Singh
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - David Davidson
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Gerd Prehna
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
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3
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Somarathne RP, Amarasekara DL, Kariyawasam CS, Robertson HA, Mayatt R, Gwaltney SR, Fitzkee NC. Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305684. [PMID: 38247186 PMCID: PMC11209821 DOI: 10.1002/smll.202305684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/03/2024] [Indexed: 01/23/2024]
Abstract
Understanding the conformation of proteins in the nanoparticle corona has important implications in how organisms respond to nanoparticle-based drugs. These proteins coat the nanoparticle surface, and their properties will influence the nanoparticle's interaction with cell targets and the immune system. While some coronas are thought to be disordered, two key unanswered questions are the degree of disorder and solvent accessibility. Here, a model is developed for protein corona disorder in polystyrene nanoparticles of varying size. For two different proteins, it is found that binding affinity decreases as nanoparticle size increases. The stoichiometry of binding, along with changes in the hydrodynamic size, supports a highly solvated, disordered protein corona anchored at a small number of attachment sites. The scaling of the stoichiometry versus nanoparticle size is consistent with disordered polymer dimensions. Moreover, it is found that proteins are destabilized less in the presence of larger nanoparticles, and hydrophobic exposure decreases at lower curvatures. The observations hold for proteins on flat polystyrene surfaces, which have the lowest hydrophobic exposure. The model provides an explanation for previous observations of increased amyloid fibrillation rates in the presence of larger nanoparticles, and it may rationalize how cell receptors can recognize protein disorder in therapeutic nanoparticles.
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Affiliation(s)
- Radha P Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Dhanush L Amarasekara
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Harley A Robertson
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Railey Mayatt
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Steven R Gwaltney
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
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4
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Nixon C, Lim SA, Sternke M, Barrick D, Harms MJ, Marqusee S. The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins. Protein Sci 2024; 33:e5011. [PMID: 38747388 PMCID: PMC11094778 DOI: 10.1002/pro.5011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/02/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
A protein sequence encodes its energy landscape-all the accessible conformations, energetics, and dynamics. The evolutionary relationship between sequence and landscape can be probed phylogenetically by compiling a multiple sequence alignment of homologous sequences and generating common ancestors via Ancestral Sequence Reconstruction or a consensus protein containing the most common amino acid at each position. Both ancestral and consensus proteins are often more stable than their extant homologs-questioning the differences between them and suggesting that both approaches serve as general methods to engineer thermostability. We used the Ribonuclease H family to compare these approaches and evaluate how the evolutionary relationship of the input sequences affects the properties of the resulting consensus protein. While the consensus protein derived from our full Ribonuclease H sequence alignment is structured and active, it neither shows properties of a well-folded protein nor has enhanced stability. In contrast, the consensus protein derived from a phylogenetically-restricted set of sequences is significantly more stable and cooperatively folded, suggesting that cooperativity may be encoded by different mechanisms in separate clades and lost when too many diverse clades are combined to generate a consensus protein. To explore this, we compared pairwise covariance scores using a Potts formalism as well as higher-order sequence correlations using singular value decomposition (SVD). We find the SVD coordinates of a stable consensus sequence are close to coordinates of the analogous ancestor sequence and its descendants, whereas the unstable consensus sequences are outliers in SVD space.
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Affiliation(s)
- Charlotte Nixon
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Shion A. Lim
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Matt Sternke
- The T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Doug Barrick
- The T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Michael J. Harms
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Susan Marqusee
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
- Department of ChemistryUniversity of California, BerkeleyBerkeleyCaliforniaUSA
- California Institute for Quantitative Biosciences (QB3)BerkeleyCaliforniaUSA
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5
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Lin Y, Horne WS. Backbone Modification in a Protein Hydrophobic Core. Chemistry 2024:e202401890. [PMID: 38753977 DOI: 10.1002/chem.202401890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/18/2024]
Abstract
Targeted protein backbone modification can recreate tertiary structures reminiscent of folds found in nature on artificial scaffolds with improved biostability. Incorporation of altered monomers in such entities is typically limited to sites distant from the hydrophobic core to avoid potential disruptions to folding. This is limiting, as it is advantageous in some applications to incorporate artificial connectivity at buried sites. Here, we report an examination of protein backbone modification targeted specifically to hydrophobic core positions and its impacts on tertiary folded structure and fold stability. Different artificial monomer types are placed at core, core-flanking, or solvent-exposed positions in a compact three-helix protein. Effects on structure and folding energetics are assessed by NMR spectroscopy and biophysical methods. Results show that artificial residues can be well accommodated in the hydrophobic core of a defined tertiary fold, with effects on stability only modestly larger than identical changes at solvent-exposed sites. Collectively, these results provide new insights into folding behavior of protein-like artificial chains as well as strategies for the design of such molecules.
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Affiliation(s)
- Yuhan Lin
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA
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6
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Wu T, Yu JC, Suresh A, Gale-Day ZJ, Alteen MG, Woo AS, Millbern Z, Johnson OT, Carroll EC, Partch CL, Fourches D, Vinueza NR, Vocadlo DJ, Gestwicki JE. Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes. Nat Biotechnol 2024:10.1038/s41587-024-02158-7. [PMID: 38744946 DOI: 10.1038/s41587-024-02158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/31/2024] [Indexed: 05/16/2024]
Abstract
Differential scanning fluorimetry (DSF) is a technique that reports protein thermal stability via the selective recognition of unfolded states by fluorogenic dyes. However, DSF applications remain limited by protein incompatibilities with existing DSF dyes. Here we overcome this obstacle with the development of a protein-adaptive DSF platform (paDSF) that combines a dye library 'Aurora' with a streamlined procedure to identify protein-dye pairs on demand. paDSF was successfully applied to 94% (66 of 70) of proteins, tripling the previous compatibility and delivering assays for 66 functionally and biochemically diverse proteins, including 10 from severe acute respiratory syndrome coronavirus 2. We find that paDSF can be used to monitor biological processes that were previously inaccessible, demonstrated for the interdomain allostery of O-GlcNAc transferase. The chemical diversity and varied selectivities of Aurora dyes suggest that paDSF functionality may be readily extended. paDSF is a generalizable tool to interrogate protein stability, dynamics and ligand binding.
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Affiliation(s)
- Taiasean Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Joshua C Yu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Arundhati Suresh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Zachary J Gale-Day
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Matthew G Alteen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Amanda S Woo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Zoe Millbern
- Department of Textile Engineering, North Carolina State University, Raleigh, NC, USA
| | - Oleta T Johnson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Emma C Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Carrie L Partch
- Department of Chemistry, University of California, Santa Cruz, CA, USA
| | - Denis Fourches
- Department of Textile Engineering, North Carolina State University, Raleigh, NC, USA
| | - Nelson R Vinueza
- Department of Textile Engineering, North Carolina State University, Raleigh, NC, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA.
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7
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Baxa MC, Lin X, Mukinay CD, Chakravarthy S, Sachleben JR, Antilla S, Hartrampf N, Riback JA, Gagnon IA, Pentelute BL, Clark PL, Sosnick TR. How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins. Protein Sci 2024; 33:e4986. [PMID: 38607226 PMCID: PMC11010952 DOI: 10.1002/pro.4986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.
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Affiliation(s)
- Michael C. Baxa
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Xiaoxuan Lin
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Cedrick D. Mukinay
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team (BioCAT), Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical SciencesIllinois Institute of TechnologyChicagoIllinoisUSA
- Present address:
Cytiva, Fast TrakMarlboroughMAUSA
| | | | - Sarah Antilla
- Department of Materials Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Nina Hartrampf
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
Department of ChemistryUniversity of ZurichSwitzerland
| | - Joshua A. Riback
- Graduate Program in Biophysical ScienceUniversity of ChicagoChicagoIllinoisUSA
- Present address:
Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
| | - Isabelle A. Gagnon
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
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8
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Lauzon D, Vallée-Bélisle A. Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies. Angew Chem Int Ed Engl 2024; 63:e202313944. [PMID: 37975629 DOI: 10.1002/anie.202313944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Most functional nanosystems in living organisms are constructed using multimeric assemblies that provide multiple advantages over their monomeric counterparts such as cooperative or anti-cooperative responses, integration of multiple signals and self-regulation. Inspired by these natural nanosystems, chemists have been synthesizing self-assembled supramolecular systems over the last 50 years with increasing complexity with applications ranging from biosensing, drug delivery, synthetic biology, and system chemistry. Although many advances have been made concerning the design principles of novel molecular architectures and chemistries, little is still known, however, about how to program their dynamic of assembly so that they can assemble at the required concentration and with the right sensitivity. Here, we used synthetic DNA assemblies and double-mutant cycle analysis to explore the thermodynamic basis to program the cooperativity of molecular assemblies. The results presented here exemplify how programmable molecular assemblies can be efficiently built by fusing interacting domains and optimizing their compaction. They may also provide the rational basis for understanding the thermodynamic and mechanistic principles driving the evolution of multimeric biological complexes.
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Affiliation(s)
- Dominic Lauzon
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
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9
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Koch J, Romero‐Romero S, Höcker B. Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novo TIM barrels. Protein Sci 2024; 33:e4926. [PMID: 38380781 PMCID: PMC10880431 DOI: 10.1002/pro.4926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
Over the past decades, the TIM-barrel fold has served as a model system for the exploration of how changes in protein sequences affect their structural, stability, and functional characteristics, and moreover, how this information can be leveraged to design proteins from the ground up. After numerous attempts to design de novo proteins with this specific fold, sTIM11 was the first validated de novo design of an idealized four-fold symmetric TIM barrel. Subsequent efforts to enhance the stability of this initial design resulted in the development of DeNovoTIMs, a family of de novo TIM barrels with various stabilizing mutations. In this study, we present an investigation into the biophysical and thermodynamic effects upon introducing a varying number of stabilizing mutations per quarter along the sequence of a four-fold symmetric TIM barrel. We compared the base design DeNovoTIM0 without any stabilizing mutations with variants containing mutations in one, two, three, and all four quarters-designated TIM1q, TIM2q, TIM3q, and DeNovoTIM6, respectively. This analysis revealed a stepwise and nonlinear change in the thermodynamic properties that correlated with the number of mutated quarters, suggesting positive nonadditive effects. To shed light on the significance of the location of stabilized quarters, we engineered two variants of TIM2q which contain the same number of mutations but positioned in different quarter locations. Characterization of these TIM2q variants revealed that the mutations exhibit varying effects on the overall protein stability, contingent upon the specific region in which they are introduced. These findings emphasize that the amount and location of stabilized interfaces among the four quarters play a crucial role in shaping the conformational stability of these four-fold symmetric TIM barrels. Analysis of de novo proteins, as described in this study, enhances our understanding of how sequence variations can finely modulate stability in both naturally occurring and computationally designed proteins.
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Affiliation(s)
| | | | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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10
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Sakuma K, Kobayashi N, Sugiki T, Nagashima T, Fujiwara T, Suzuki K, Kobayashi N, Murata T, Kosugi T, Tatsumi-Koga R, Koga N. Design of complicated all-α protein structures. Nat Struct Mol Biol 2024; 31:275-282. [PMID: 38177681 DOI: 10.1038/s41594-023-01147-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
A wide range of de novo protein structure designs have been achieved, but the complexity of naturally occurring protein structures is still far beyond these designs. Here, to expand the diversity and complexity of de novo designed protein structures, we sought to develop a method for designing 'difficult-to-describe' α-helical protein structures composed of irregularly aligned α-helices like globins. Backbone structure libraries consisting of a myriad of α-helical structures with five or six helices were generated by combining 18 helix-loop-helix motifs and canonical α-helices, and five distinct topologies were selected for de novo design. The designs were found to be monomeric with high thermal stability in solution and fold into the target topologies with atomic accuracy. This study demonstrated that complicated α-helical proteins are created using typical building blocks. The method we developed will enable us to explore the universe of protein structures for designing novel functional proteins.
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Affiliation(s)
- Koya Sakuma
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Naohiro Kobayashi
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
- Institute for Protein Research, Osaka University, Suita, Japan
| | | | - Toshio Nagashima
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | | | - Kano Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Naoya Kobayashi
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of National Sciences, Okazaki, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Membrane Protein Research Center, Chiba University, Chiba, Japan
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Takahiro Kosugi
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of National Sciences, Okazaki, Japan
- Research Center of Integrative Molecular Systems, Institute for Molecular Science, National Institutes of National Sciences, Okazaki, Japan
| | - Rie Tatsumi-Koga
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of National Sciences, Okazaki, Japan
| | - Nobuyasu Koga
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan.
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of National Sciences, Okazaki, Japan.
- Research Center of Integrative Molecular Systems, Institute for Molecular Science, National Institutes of National Sciences, Okazaki, Japan.
- Institute for Protein Research, Osaka University, Suita, Japan.
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11
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Villanueva M, Vostal LE, Cohen DN, Biesbrock D, Kuwaye EP, Driver SG, Hart KM. Differential effects of disulfide bond formation in TEM-1 versus CTX-M-9 β-lactamase. Protein Sci 2024; 33:e4816. [PMID: 37897253 PMCID: PMC10731493 DOI: 10.1002/pro.4816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
To investigate how disulfide bonds can impact protein energy landscapes, we surveyed the effects of adding or removing a disulfide in two β-lactamase enzymes, TEM-1 and CTX-M-9. The homologs share a structure and 38% sequence identity, but only TEM-1 contains a native disulfide bond. They also differ in thermodynamic stability and in the number of states populated at equilibrium: CTX-M-9 is two-state whereas TEM-1 has an additional intermediate state. We hypothesized that the disulfide bond is the major underlying determinant for these observed differences in their energy landscapes. To test this, we removed the disulfide bridge from TEM-1 and introduced a disulfide bridge at the same location in CTX-M-9. This modest change to sequence modulates the stabilities-and therefore populations-of TEM-1's equilibrium states and, more surprisingly, creates a novel third state in CTX-M-9. Unlike TEM-1's partially folded intermediate, this third state is a higher-order oligomer with reduced cysteines that retains the native fold and is fully active. Sub-denaturing concentrations of urea shifts the equilibrium to the monomeric form, allowing the disulfide bond to form. Interestingly, comparing the stability of the oxidized monomer with a variant lacking cysteines reveals the disulfide is neither stabilizing nor destabilizing in CTX-M-9, in contrast with the observed stabilization in TEM-1. Thus, we can conclude that engineering disulfide bonds is not always an effective stabilization strategy even when analogous disulfides exist in more stable structural homologs. This study also illustrates how homo-oligomerization can result from a small number of mutations, suggesting complex formation might be easily accessed during a protein family's evolution.
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Affiliation(s)
- Miranda Villanueva
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Biological Chemistry DepartmentDavid Geffen School of Medicine, UCLALos AngelesCaliforniaUSA
| | - Lauren E. Vostal
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Chemistry and Cell BiologyThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Drew N. Cohen
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Devin Biesbrock
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Cellular and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Elise P. Kuwaye
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Department of Biological SciencesColumbia UniversityNew YorkNew YorkUSA
| | - Sasha G. Driver
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
| | - Kathryn M. Hart
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
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12
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Narsimulu B, Jakkula P, Qureshi R, Nasim F, Qureshi IA. Inhibition and structural insights of leishmanial glutamyl-tRNA synthetase for designing potent therapeutics. Int J Biol Macromol 2024; 254:127756. [PMID: 37907177 DOI: 10.1016/j.ijbiomac.2023.127756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/08/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs), essential components of the protein synthesizing machinery, have been often chosen for devising therapeutics against parasitic diseases. Due to their relevance in drug development, the current study was designed to explore functional and structural aspects of Leishmania donovani glutamyl-tRNA synthetase (LdGluRS). Hence, LdGluRS was cloned into an expression vector and purified to homogeneity using chromatographic techniques. Purified protein showed maximum enzymatic activity at physiological pH, with more binding capacity towards its cofactor (Adenosine triphosphate, 0.06 ± 0.01 mM) than the cognate substrate (L-glutamate, 9.5 ± 0.5 mM). Remarkably, salicylate inhibited LdGluRS competitively with respect to L-glutamate and exhibited druglikeness with negligible effect on human macrophages. The protein possessed more α-helices (43 %) than β-sheets (12 %), whereas reductions in thermal stability and cofactor-binding affinity, along with variation in mode of inhibition after mutation signified the role of histidine (H60) as a catalytic residue. LdGluRS could also generate a pro-inflammatory milieu in human macrophages by upregulating cytokines. The docking study demonstrated the placement of salicylate into LdGluRS substrate-binding site, and the complex was found to be stable during molecular dynamics (MD) simulation. Altogether, our study highlights the understanding of molecular inhibition and structural features of glutamyl-tRNA synthetase from kinetoplastid parasites.
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Affiliation(s)
- Bandigi Narsimulu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Pranay Jakkula
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Rahila Qureshi
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Fouzia Nasim
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India.
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13
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Hervø-Hansen S, Polák J, Tomandlová M, Dzubiella J, Heyda J, Lund M. Salt Effects on Caffeine across Concentration Regimes. J Phys Chem B 2023; 127:10253-10265. [PMID: 38058160 DOI: 10.1021/acs.jpcb.3c01085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Salts affect the solvation thermodynamics of molecules of all sizes; the Hofmeister series is a prime example in which different ions lead to salting-in or salting-out of aqueous proteins. Early work of Tanford led to the discovery that the solvation of molecular surface motifs is proportional to the solvent accessible surface area (SASA), and later studies have shown that the proportionality constant varies with the salt concentration and type. Using multiscale computer simulations combined with vapor-pressure osmometry on caffeine-salt solutions, we reveal that this SASA description captures a rich set of molecular driving forces in tertiary solutions at changing solute and osmolyte concentrations. Central to the theoretical work is a new potential energy function that depends on the instantaneous surface area, salt type, and concentration. Used in, e.g., Monte Carlo simulations, this allows for a highly efficient exploration of many-body interactions and the resulting thermodynamics at elevated solute and salt concentrations.
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Affiliation(s)
- Stefan Hervø-Hansen
- Division of Computational Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Markéta Tomandlová
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Joachim Dzubiella
- Physikalisches Institut, Albert-Ludwigs Universität Freiburg, Hermann-Herder-Straße 3, Freiburg Im Breisgau D-79104, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Mikael Lund
- Division of Computational Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
- Lund Institute of Advance Neutron and X-ray Science (LINXS), Lund SE 223 70, Sweden
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14
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Acquasaliente L, Pierangelini A, Pagotto A, Pozzi N, De Filippis V. From haemadin to haemanorm: Synthesis and characterization of full-length haemadin from the leech Haemadipsa sylvestris and of a novel bivalent, highly potent thrombin inhibitor (haemanorm). Protein Sci 2023; 32:e4825. [PMID: 37924304 PMCID: PMC10683372 DOI: 10.1002/pro.4825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Hirudin from Hirudo medicinalis is a bivalent α-Thrombin (αT) inhibitor, targeting the enzyme active site and exosite-I, and is currently used in anticoagulant therapy along with its simplified analogue hirulog. Haemadin, a small protein (57 amino acids) isolated from the land-living leech Haemadipsa sylvestris, selectively inhibits αT with a potency identical to that of recombinant hirudin (KI = 0.2 pM), with which it shares a common disulfide topology and overall fold. At variance with hirudin, haemadin targets exosite-II and therefore (besides the free protease) it also blocks thrombomodulin-bound αT without inhibiting the active intermediate meizothrombin, thus offering potential advantages over hirudin. Here, we produced in reasonably high yields and pharmaceutical purity (>98%) wild-type haemadin and the oxidation resistant Met5 → nor-Leucine analogue, both inhibiting αT with a KI of 0.2 pM. Thereafter, we used site-directed mutagenesis, spectroscopic, ligand-displacement, and Hydrogen/Deuterium Exchange-Mass Spectrometry techniques to map the αT regions relevant for the interaction with full-length haemadin and with the synthetic N- and C-terminal peptides Haem(1-10) and Haem(45-57). Haem(1-10) competitively binds to/inhibits αT active site (KI = 1.9 μM) and its potency was enhanced by 10-fold after Phe3 → β-Naphthylalanine exchange. Conversely to full-length haemadin, haem(45-57) displays intrinsic affinity for exosite-I (KD = 1.6 μM). Hence, we synthesized a peptide in which the sequences 1-9 and 45-57 were joined together through a 3-Glycine spacer to yield haemanorm, a highly potent (KI = 0.8 nM) inhibitor targeting αT active site and exosite-I. Haemanorm can be regarded as a novel class of hirulog-like αT inhibitors with potential pharmacological applications.
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Affiliation(s)
- Laura Acquasaliente
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Andrea Pierangelini
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Anna Pagotto
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Nicola Pozzi
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research CenterSaint Louis UniversitySt. LouisMissouriUSA
| | - Vincenzo De Filippis
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
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15
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Das D, Ainavarapu SRK. Circular permutation at azurin's active site slows down its folding. J Biol Inorg Chem 2023; 28:737-749. [PMID: 37957357 DOI: 10.1007/s00775-023-02023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Circular permutation (CP) is a technique by which the primary sequence of a protein is rearranged to create new termini. The connectivity of the protein is altered but the overall protein structure generally remains unperturbed. Understanding the effect of CP can help design robust proteins for numerous applications such as in genetic engineering, optoelectronics, and improving catalytic activity. Studies on different protein topologies showed that CP usually affects protein stability as well as unfolding rates. Though a significant number of proteins contain metals or other cofactors, reports of metalloprotein CPs are rare. Thus, we chose a bacterial metalloprotein, azurin, and its CP within the metal-binding site (cpF114). We studied the stabilities, folding, and unfolding rates of apo- and Zn2+-bound CP azurin using fluorescence and circular dichroism. The introduced CP had destabilizing effects on the protein. Also, the folding of the Zn2+-CP protein was much slower than that of the Zn2+-WT or apo-protein. We compared this study to our previously reported azurin-cpN42, where we had observed an equilibrium and kinetic intermediate. cpF114 exhibits an apparent two-state equilibrium unfolding but has an off-pathway kinetic intermediate. Our study hinted at CP as a method to modify the energy landscape of proteins to alter their folding pathways. WT azurin, being a faster folder, may have evolved to optimize the folding rate of metal-bound protein compared to its CPs, albeit all of them have the same structure and function. Our study underscores that protein sequence and protein termini positions are crucial for metalloproteins. TOC Figure. (Top) Zn2+-azurin WT structure (PDB code: 1E67) and 2-D topology diagram of Zn2+-cpF114 azurin. (Bottom) Cartoon diagram representing folding (red arrows) and unfolding (blue arrows) of apo- and Zn2+- WT and cpF114 azurins. The width of the arrows represents the rate of the corresponding processes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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16
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Musil M, Jezik A, Horackova J, Borko S, Kabourek P, Damborsky J, Bednar D. FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Brief Bioinform 2023; 25:bbad425. [PMID: 38018911 PMCID: PMC10685400 DOI: 10.1093/bib/bbad425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable proteins often results in single-point mutations with a limited effect on protein stability. However, the construction of stable multiple-point mutants can prove difficult due to the possibility of antagonistic effects between individual mutations. FireProt protocol enables the automated computational design of highly stable multiple-point mutants. FireProt 2.0 builds on top of the previously published FireProt web, retaining the original functionality and expanding it with several new stabilization strategies. FireProt 2.0 integrates the AlphaFold database and the homology modeling for structure prediction, enabling calculations starting from a sequence. Multiple-point designs are constructed using the Bron-Kerbosch algorithm minimizing the antagonistic effect between the individual mutations. Users can newly limit the FireProt calculation to a set of user-defined mutations, run a saturation mutagenesis of the whole protein or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical user interface broadens the tool's availability even to users with older hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.
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Affiliation(s)
- Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Andrej Jezik
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Jana Horackova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
| | - Simeon Borko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Petr Kabourek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
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17
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Rat C, Heindl C, Neuweiler H. Domain swap facilitates structural transitions of spider silk protein C-terminal domains. Protein Sci 2023; 32:e4783. [PMID: 37712205 PMCID: PMC10578117 DOI: 10.1002/pro.4783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/25/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
Domain swap is a mechanism of protein dimerization where the two interacting domains exchange parts of their structure. Web spiders make use of the process in the connection of C-terminal domains (CTDs) of spidroins, the soluble protein building blocks that form tough silk fibers. Besides providing connectivity and solubility, spidroin CTDs are responsible for inducing structural transitions during passage through an acidified assembly zone within spinning ducts. The underlying molecular mechanisms are elusive. Here, we studied the folding of five homologous spidroin CTDs from different spider species or glands. Four of these are domain-swapped dimers formed by five-helix bundles from spidroins of major and minor ampullate glands. The fifth is a dimer that lacks domain swap, formed by four-helix bundles from a spidroin of a flagelliform gland. Spidroins from this gland do not undergo structural transitions whereas the others do. We found a three-state mechanism of folding and dimerization that was conserved across homologues. In chemical denaturation experiments the native CTD dimer unfolded to a dimeric, partially structured intermediate, followed by full unfolding to denatured monomers. The energetics of the individual folding steps varied between homologues. Contrary to the common belief that domain swap stabilizes protein assemblies, the non-swapped homologue was most stable and folded four orders of magnitude faster than a swapped variant. Domain swap of spidroin CTDs induces an entropic penalty to the folding of peripheral helices, thus unfastening them for acid-induced unfolding within a spinning duct, which primes them for refolding into alternative structures during silk formation.
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Affiliation(s)
- Charlotte Rat
- Department of Biotechnology & BiophysicsJulius‐Maximilians‐University WürzburgWürzburgGermany
| | - Cedric Heindl
- Department of Biotechnology & BiophysicsJulius‐Maximilians‐University WürzburgWürzburgGermany
| | - Hannes Neuweiler
- Department of Biotechnology & BiophysicsJulius‐Maximilians‐University WürzburgWürzburgGermany
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18
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Posey AE, Ross KA, Bagheri M, Lanum EN, Khan MA, Jennings CE, Harwig MC, Kennedy NW, Hilser VJ, Harden JL, Hill RB. The variable domain from dynamin-related protein 1 promotes liquid-liquid phase separation that enhances its interaction with cardiolipin-containing membranes. Protein Sci 2023; 32:e4787. [PMID: 37743569 PMCID: PMC10578129 DOI: 10.1002/pro.4787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" important for regulation. For the mitochondrial fission dynamin, dynamin-related protein 1, a regulatory role for the variable domain (VD) is demonstrated by gain- and loss-of-function mutations, yet the basis for this is unclear. Here, the isolated VD is shown to be intrinsically disordered and undergo a cooperative transition in the stabilizing osmolyte trimethylamine N-oxide. However, the osmolyte-induced state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, which appears to promote phase separation. Since dynamin-related protein 1 is found assembled into discrete punctate structures on the mitochondrial surface, the inference from the present work is that these structures might arise from a condensed state involving the VD that may enable rapid tuning of mechanoenzyme assembly necessary for fission.
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Affiliation(s)
- Ammon E. Posey
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
- Present address:
Department of Biomedical EngineeringWashington UniversitySt. LouisMissouriUSA
| | - Kyle A. Ross
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Mehran Bagheri
- Department of PhysicsUniversity of OttawaOttawaOntarioUSA
| | - Elizabeth N. Lanum
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Misha A. Khan
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | - Megan C. Harwig
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Nolan W. Kennedy
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Vincent J. Hilser
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | | | - R. Blake Hill
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
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19
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Pennacchietti V, Pagano L, Malagrinò F, Diop A, Di Felice M, Di Matteo S, Marcocci L, Pietrangeli P, Toto A, Gianni S. Characterization of the folding and binding properties of the PTB domain of FRS2 with phosphorylated and unphosphorylated ligands. Arch Biochem Biophys 2023; 745:109703. [PMID: 37543351 DOI: 10.1016/j.abb.2023.109703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
PTB (PhosphoTyrosine Binding) domains are protein domains that exert their function by binding phosphotyrosine residues on other proteins. They are commonly found in a variety of signaling proteins and are important for mediating protein-protein interactions in numerous cellular processes. PTB domains can also exhibit binding to unphosphorylated ligands, suggesting that they have additional binding specificities beyond phosphotyrosine recognition. Structural studies have reported that the PTB domain from FRS2 possesses this peculiar feature, allowing it to interact with both phosphorylated and unphosphorylated ligands, such as TrkB and FGFR1, through different topologies and orientations. In an effort to elucidate the dynamic and functional properties of these protein-protein interactions, we provide a complete characterization of the folding mechanism of the PTB domain of FRS2 and the binding process to peptides mimicking specific regions of TrkB and FGFR1. By analyzing the equilibrium and kinetics of PTB folding, we propose a mechanism implying the presence of an intermediate along the folding pathway. Kinetic binding experiments performed at different ionic strengths highlighted the electrostatic nature of the interaction with both peptides. The specific role of single amino acids in early and late events of binding was pinpointed by site-directed mutagenesis. These results are discussed in light of previous experimental works on these protein systems.
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Affiliation(s)
- Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Livia Pagano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Francesca Malagrinò
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Awa Diop
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Mariana Di Felice
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Sara Di Matteo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Lucia Marcocci
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Paola Pietrangeli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy.
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy.
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20
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Tan R, Hoare M, Welle KA, Swovick K, Hryhorenko JR, Ghaemmaghami S. Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry. Proc Natl Acad Sci U S A 2023; 120:e2303167120. [PMID: 37552756 PMCID: PMC10438377 DOI: 10.1073/pnas.2303167120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/11/2023] [Indexed: 08/10/2023] Open
Abstract
The folding of most proteins occurs during the course of their translation while their tRNA-bound C termini are embedded in the ribosome. How the close proximity of nascent proteins to the ribosome influences their folding thermodynamics remains poorly understood. Here, we have developed a mass spectrometry-based approach for determining the stabilities of nascent polypeptide chains using methionine oxidation as a folding probe. This approach enables quantitative measurement subglobal folding stabilities of ribosome nascent chains within complex protein mixtures and extracts. To validate the methodology, we analyzed the folding thermodynamics of three model proteins (dihydrofolate reductase, chemotaxis protein Y, and DNA polymerase IV) in soluble and ribosome-bound states. The data indicate that the ribosome can significantly alter the stability of nascent polypeptides. Ribosome-induced stability modulations were highly variable among different folding domains and were dependent on localized charge distributions within nascent polypeptides. The results implicated electrostatic interactions between the ribosome surface and nascent polypeptides as the cause of ribosome-induced stability modulations. The study establishes a robust proteomic methodology for analyzing localized stabilities within ribosome-bound nascent polypeptides and sheds light on how the ribosome influences the thermodynamics of protein folding.
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Affiliation(s)
- Ruiyue Tan
- Department of Biology, University of Rochester, Rochester, NY14627
| | - Margaret Hoare
- Department of Biology, University of Rochester, Rochester, NY14627
| | - Kevin A. Welle
- Mass Spectrometry Resource Laboratory, University of Rochester Medical Center, Rochester, NY14627
| | - Kyle Swovick
- Mass Spectrometry Resource Laboratory, University of Rochester Medical Center, Rochester, NY14627
| | - Jennifer R. Hryhorenko
- Mass Spectrometry Resource Laboratory, University of Rochester Medical Center, Rochester, NY14627
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, Rochester, NY14627
- Mass Spectrometry Resource Laboratory, University of Rochester Medical Center, Rochester, NY14627
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21
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Martinez Grundman JE, Johnson EA, Lecomte JTJ. Architectural digest: Thermodynamic stability and domain structure of a consensus monomeric globin. Biophys J 2023; 122:3117-3132. [PMID: 37353934 PMCID: PMC10432219 DOI: 10.1016/j.bpj.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Artificial proteins representing the consensus of a set of homologous sequences have attracted attention for their increased thermodynamic stability and conserved activity. Here, we applied the consensus approach to a b-type heme-binding protein to inspect the contribution of a dissociable cofactor to enhanced stability and the chemical consequences of creating a generic heme environment. We targeted the group 1 truncated hemoglobin (TrHb1) subfamily of proteins for their small size (∼120 residues) and ease of characterization. The primary structure, derived from a curated set of ∼300 representative sequences, yielded a highly soluble consensus globin (cGlbN) enriched in acidic residues. Optical and NMR spectroscopies revealed high-affinity heme binding in the expected site and in two orientations. At neutral pH, proximal and distal iron coordination was achieved with a pair of histidine residues, as observed in some natural TrHb1s, and with labile ligation on the distal side. As opposed to studied TrHb1s, which undergo additional folding upon heme binding, cGlbN displayed the same extent of secondary structure whether the heme was associated with the protein or not. Denaturation required guanidine hydrochloride and showed that apo- and holoprotein unfolded in two transitions-the first (occurring with a midpoint of ∼2 M) was shifted to higher denaturant concentration in the holoprotein (∼3.7 M) and reflected stabilization due to heme binding, while the second transition (∼6.2 M) was common to both forms. Thus, the consensus sequence stabilized the protein but exposed the existence of two separately cooperative subdomains within the globin architecture, masked as one single domain in TrHb1s with typical stabilities. The results suggested ways in which specific chemical or thermodynamic features may be controlled in artificial heme proteins.
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Affiliation(s)
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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22
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Somarathne RP, Amarasekara DL, Kariyawasam CS, Robertson HA, Mayatt R, Fitzkee NC. Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548033. [PMID: 37461509 PMCID: PMC10350082 DOI: 10.1101/2023.07.06.548033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Understanding the conformation of proteins in the nanoparticle corona has important implications in how organisms respond to nanoparticle-based drugs. These proteins coat the nanoparticle surface, and their properties will influence the nanoparticle's interaction with cell targets and the immune system. While some coronas are thought to be disordered, two key unanswered questions are the degree of disorder and solvent accessibility. Here, using a comprehensive thermodynamic approach, along with supporting spectroscopic experiments, we develop a model for protein corona disorder in polystyrene nanoparticles of varying size. For two different proteins, we find that binding affinity decreases as nanoparticle size increases. The stoichiometry of binding, along with changes in the hydrodynamic size, support a highly solvated, disordered protein corona anchored at a small number of enthalpically-driven attachment sites. The scaling of the stoichiometry vs. nanoparticle size is consistent disordered polymer dimensions. Moreover, we find that proteins are destabilized less severely in the presence of larger nanoparticles, and this is supported by measurements of hydrophobic exposure, which becomes less pronounced at lower curvatures. Our observations hold for flat polystyrene surfaces, which, when controlled for total surface area, have the lowest hydrophobic exposure of all systems. Our model provides an explanation for previous observations of increased amyloid fibrillation rates in the presence of larger nanoparticles, and it may rationalize how cell receptors can recognize protein disorder in therapeutic nanoparticles.
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Affiliation(s)
- Radha P. Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | | | | | - Harley A. Robertson
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | - Railey Mayatt
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
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23
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Villalobos P, Carvajal AI, Castro-Fernández V, Babul J, Ramírez-Sarmiento CA, Medina E. Unraveling the folding and dimerization properties of the human FoxP subfamily of transcription factors. FEBS Lett 2023; 597:1894-1905. [PMID: 37199668 DOI: 10.1002/1873-3468.14665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Human FoxP proteins share a highly conserved DNA-binding domain that dimerizes via three-dimensional domain swapping, although showing varying oligomerization propensities among its members. Here, we present an experimental and computational characterization of all human FoxP proteins to unravel how their amino acid substitutions impact their folding and dimerization mechanism. We solved the crystal structure of the forkhead domain of FoxP4 to then perform a comparison across all members, finding that their sequence changes impact not only the structural heterogeneity of their forkhead domains but also the protein-protein association energy barrier. Lastly, we demonstrate that the accumulation of a monomeric intermediate is an oligomerization-dependent feature rather than a common aspect of monomers and dimers in this protein subfamily.
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Affiliation(s)
- Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alonso I Carvajal
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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24
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Nixon C, Lim SA, Sternke M, Barrick D, Harms M, Marqusee S. The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547063. [PMID: 37425932 PMCID: PMC10327145 DOI: 10.1101/2023.06.29.547063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
A protein sequence encodes its energy landscape - all the accessible conformations, energetics, and dynamics. The evolutionary relationship between sequence and landscape can be probed phylogenetically by compiling a multiple sequence alignment of homologous sequences and generating common ancestors via Ancestral Sequence Reconstruction or a consensus protein containing the most common amino acid at each position. Both ancestral and consensus proteins are often more stable than their extant homologs - questioning the differences and suggesting that both approaches serve as general methods to engineer thermostability. We used the Ribonuclease H family to compare these approaches and evaluate how the evolutionary relationship of the input sequences affects the properties of the resulting consensus protein. While the overall consensus protein is structured and active, it neither shows properties of a well-folded protein nor has enhanced stability. In contrast, the consensus protein derived from a phylogenetically-restricted region is significantly more stable and cooperatively folded, suggesting that cooperativity may be encoded by different mechanisms in separate clades and lost when too many diverse clades are combined to generate a consensus protein. To explore this, we compared pairwise covariance scores using a Potts formalism as well as higher-order couplings using singular value decomposition (SVD). We find the SVD coordinates of a stable consensus sequence are close to coordinates of the analogous ancestor sequence and its descendants, whereas the unstable consensus sequences are outliers in SVD space.
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Affiliation(s)
- Charlotte Nixon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Shion A Lim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Matt Sternke
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Doug Barrick
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Mike Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), Berkeley
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25
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López‐Pérez E, de Gómez‐Puyou MT, Nuñez CJ, Zapién DM, Guardado SA, Beltrán HI, Pérez‐Hernández G. Ordered-domain unfolding of thermophilic isolated β subunit ATP synthase. Protein Sci 2023; 32:e4689. [PMID: 37252686 PMCID: PMC10273367 DOI: 10.1002/pro.4689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023]
Abstract
The flexibility of the ATP synthase's β subunit promotes its role in the ATP synthase rotational mechanism, but its domains stability remains unknown. A reversible thermal unfolding of the isolated β subunit (Tβ) of the ATP synthase from Bacillus thermophilus PS3, tracked through circular dichroism and molecular dynamics, indicated that Tβ shape transits from an ellipsoid to a molten globule through an ordered unfolding of its domains, preserving the β-sheet residual structure at high temperature. We determined that part of the stability origin of Tβ is due to a transversal hydrophobic array that crosses the β-barrel formed at the N-terminal domain and the Rossman fold of the nucleotide-binding domain (NBD), while the helix bundle of the C-terminal domain is the less stable due to the lack of hydrophobic residues, and thus the more flexible to trigger the rotational mechanism of the ATP synthase.
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Affiliation(s)
- Edgar López‐Pérez
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Marietta Tuena de Gómez‐Puyou
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Concepción José Nuñez
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Denise Martínez Zapién
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Salomón Alas Guardado
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Hiram Isaac Beltrán
- División de Ciencias Básicas e Ingeniería, Departamento de Ciencias BásicasUniversidad Autónoma Metropolitana, Unidad AzcapotzalcoCiudad de MéxicoMexico
| | - Gerardo Pérez‐Hernández
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
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26
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Cordes MHJ, Sundman AK, Fox HC, Binford GJ. Protein salvage and repurposing in evolution: Phospholipase D toxins are stabilized by a remodeled scrap of a membrane association domain. Protein Sci 2023; 32:e4701. [PMID: 37313620 PMCID: PMC10303701 DOI: 10.1002/pro.4701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023]
Abstract
The glycerophosphodiester phosphodiesterase (GDPD)-like SMaseD/PLD domain family, which includes phospholipase D (PLD) toxins in recluse spiders and actinobacteria, evolved anciently in bacteria from the GDPD. The PLD enzymes retained the core (β/α)8 barrel fold of GDPD, while gaining a signature C-terminal expansion motif and losing a small insertion domain. Using sequence alignments and phylogenetic analysis, we infer that the C-terminal motif derives from a segment of an ancient bacterial PLAT domain. Formally, part of a protein containing a PLAT domain repeat underwent fusion to the C terminus of a GDPD barrel, leading to attachment of a segment of a PLAT domain, followed by a second complete PLAT domain. The complete domain was retained only in some basal homologs, but the PLAT segment was conserved and repurposed as the expansion motif. The PLAT segment corresponds to strands β7-β8 of a β-sandwich, while the expansion motif as represented in spider PLD toxins has been remodeled as an α-helix, a β-strand, and an ordered loop. The GDPD-PLAT fusion led to two acquisitions in founding the GDPD-like SMaseD/PLD family: (1) a PLAT domain that presumably supported early lipase activity by mediating membrane association, and (2) an expansion motif that putatively stabilized the catalytic domain, possibly compensating for, or permitting, loss of the insertion domain. Of wider significance, messy domain shuffling events can leave behind scraps of domains that can be salvaged, remodeled, and repurposed.
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Affiliation(s)
| | | | - Holden C. Fox
- Department of Chemistry and BiochemistryUniversity of ArizonaTucsonArizonaUSA
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27
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Posey AE, Bagheri M, Ross KA, Lanum EN, Khan MA, Jennings CM, Harwig MC, Kennedy NW, Hilser VJ, Harden JL, Hill RB. The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542732. [PMID: 37398258 PMCID: PMC10312466 DOI: 10.1101/2023.05.29.542732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" (VD) important for regulation. For the mitochondrial fission dynamin, Drp1, a regulatory role for the VD is demonstrated by mutations that can elongate, or fragment, mitochondria. How the VD encodes inhibitory and stimulatory activity is unclear. Here, isolated VD is shown to be intrinsically disordered (ID) yet undergoes a cooperative transition in the stabilizing osmolyte TMAO. However, the TMAO stabilized state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, raising the possibility that phase separation may enable rapid tuning of Drp1 assembly necessary for fission.
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28
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Giacon N, Lo Cascio E, Davidson DS, Polêto MD, Lemkul JA, Pennacchietti V, Pagano L, Zamparelli C, Toto A, Arcovito A. Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein. Comput Struct Biotechnol J 2023; 21:3259-3271. [PMID: 37293240 PMCID: PMC10210826 DOI: 10.1016/j.csbj.2023.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins in the intracellular environment. One of the main binding partners of the SARS-CoV-2 E protein is the PDZ2 domain of ZO1, a protein with a crucial role in the formation of epithelial and endothelial tight junctions (TJs). In this work, through a combination of analytical ultracentrifugation analysis and equilibrium and kinetic folding experiments, we show that ZO1-PDZ2 domain is able to fold in a monomeric state, an alternative form to the dimeric conformation that is reported to be functional in the cell for TJs assembly. Importantly, surface plasmon resonance (SPR) data indicate that the PDZ2 monomer is fully functional and capable of binding the C-terminal portion of the E protein of SARS-CoV-2, with a measured affinity in the micromolar range. Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. Together, our results indicate both the monomeric and dimeric states of PDZ2 to be functional partners of the E protein, with similar binding mechanisms, and provide mechanistic and structural information about a fundamental interaction required for the replication of SARS-CoV-2.
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Affiliation(s)
- Noah Giacon
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Darcy S. Davidson
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Marcelo D. Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Livia Pagano
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
- Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
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29
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Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
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Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
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30
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Das D, Yadav P, Mitra S, Ainavarapu SRK. Metal-binding and circular permutation-dependent thermodynamic and kinetic stability of azurin. Proteins 2023; 91:634-648. [PMID: 36511110 DOI: 10.1002/prot.26454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
Native topology is known to determine the folding kinetics and the energy landscape of proteins. Furthermore, the circular permutation (CP) of proteins alters the order of the secondary structure connectivity while retaining the three-dimensional structure, making it an elegant and powerful approach to altering native topology. Previous studies elucidated the influence of CP in proteins with different folds such as Greek key β-barrel, β-sandwich, β-α-β, and all α-Greek key. CP mainly affects the protein stability and unfolding kinetics, while folding kinetics remains mostly unaltered. However, the effect of CP on metalloproteins is yet to be elaborately studied. The active site of metalloproteins poses an additional complexity in studying protein folding. Here, we investigate a CP variant (cpN42) of azurin-in both metal-free and metal-bound (holo) forms. As observed earlier in other proteins, apo-forms of wild-type (WT) and cpN42 fold with similar rates. In contrast, zinc-binding accelerates the folding of WT but decelerates the folding of cpN42. On zinc-binding, the spontaneous folding rate of WT increases by >250 times that of cpN42, which is unprecedented and the highest for any CP to date. On the other hand, zinc-binding reduces the spontaneous unfolding rate of cpN42 by ~100 times, making the WT and CP azurins unfold at similar rates. Our study demonstrates metal binding as a novel way to modulate the unfolding and folding rates of CPs compared to their WT counterparts. We hope our study increases the understanding of the effect of CP on the folding mechanism and energy landscape of metalloproteins.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Priya Yadav
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Soumyajit Mitra
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
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31
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Gao S, Campbell JX, Oas TG, Franz KJ. Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics. Inorg Chem 2023; 62:7087-7096. [PMID: 37083393 DOI: 10.1021/acs.inorgchem.3c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Histatin 5 (Hist5) is an antimicrobial peptide found in human saliva as part of the innate immune system. Hist5 can bind several metal ions in vitro, and Zn2+ has been shown to function as an inhibitory switch to regulate the peptide's biological activity against the opportunistic fungal pathogen Candida albicans in cell culture. Here, we studied Zn2+ binding to Hist5 at four temperatures from 15 to 37 °C using isothermal titration calorimetry to obtain thermodynamic parameters that were corrected for competing buffer effects. Hist5 bound Zn2+ with a buffer-dependent association constant of ∼105 M-1 and a buffer-independent association constant of ∼6 × 106 M-1 at pH 7.4 and at all temperatures tested. Zn2+ binding was both enthalpically and entropically favorable, with larger entropic contributions at 15 °C and larger enthalpic contributions at 37 °C. Additionally, the Zn:Hist5 binding stoichiometry increased from 1:1 to 2:1 as temperature increased. The enthalpy-entropy compensation and the variable stoichiometry lead us to propose a model in which the Zn-Hist5 complex exists in an equilibrium between two distinct binding modes with different Zn:Hist5 stoichiometries. The in-depth thermodynamic analysis presented herein may help illuminate the biophysical basis for Zn-dependent changes in the antifungal activity of Hist5.
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Affiliation(s)
- Sean Gao
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Joanna X Campbell
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G Oas
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Katherine J Franz
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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32
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Seelig J, Seelig A. Protein Stability─Analysis of Heat and Cold Denaturation without and with Unfolding Models. J Phys Chem B 2023; 127:3352-3363. [PMID: 37040567 PMCID: PMC10123674 DOI: 10.1021/acs.jpcb.3c00882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Protein stability is important in many areas of life sciences. Thermal protein unfolding is investigated extensively with various spectroscopic techniques. The extraction of thermodynamic properties from these measurements requires the application of models. Differential scanning calorimetry (DSC) is less common, but is unique as it measures directly a thermodynamic property, that is, the heat capacity Cp(T). The analysis of Cp(T) is usually performed with the chemical equilibrium two-state model. This is not necessary and leads to incorrect thermodynamic consequences. Here we demonstrate a straightforward model-independent evaluation of heat capacity experiments in terms of protein unfolding enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T)). This now allows the comparison of the experimental thermodynamic data with the predictions of different models. We critically examined the standard chemical equilibrium two-state model, which predicts a positive free energy for the native protein, and diverges distinctly from the experimental temperature profiles. We propose two new models which are equally applicable to spectroscopy and calorimetry. The ΘU(T)-weighted chemical equilibrium model and the statistical-mechanical two-state model provide excellent fits of the experimental data. They predict sigmoidal temperature profiles for enthalpy and entropy, and a trapezoidal temperature profile for the free energy. This is illustrated with experimental examples for heat and cold denaturation of lysozyme and β-lactoglobulin. We then show that the free energy is not a good criterion to judge protein stability. More useful parameters are discussed, including protein cooperativity. The new parameters are embedded in a well-defined thermodynamic context and are amenable to molecular dynamics calculations.
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Affiliation(s)
- Joachim Seelig
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
| | - Anna Seelig
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
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33
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Sucharski F, Gallo G, Coelho C, Hardy L, Würtele M. Modeling the role of charged residues in thermophilic proteins by rotamer and dynamic cross correlation analysis. J Mol Model 2023; 29:132. [PMID: 37036538 DOI: 10.1007/s00894-023-05490-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/24/2023] [Indexed: 04/11/2023]
Abstract
Discerning the determinants of protein thermostability is very important both from the theoretical and applied perspective. Different lines of evidence seem to indicate that a dynamical network of salt bridges/charged residues plays a fundamental role in the thermostability of enzymes. In this work, we applied measures of dynamic variance, like the Gini coefficients, Kullback-Leibler (KL) divergence and dynamic cross correlation (DCC) coefficients to compare the behavior of 3 pairs of homologous proteins from the thermophilic bacterium Thermus thermophilus and mesophilic Escherichia coli. Molecular dynamic (MD) simulations of these proteins were performed at 303 K and 363 K. In the characterization of their side chain rotamer distributions, the corresponding Gini coefficients and KL-divergence both revealed significant correlations with temperature. Similarly, a DCC analysis revealed a higher trend to de-correlate the movement of charged residues at higher temperatures in the thermophilic proteins, when compared with their mesophilic homologues. These results highlight the importance of dynamic electrostatic network interactions for the thermostability of enzymes.
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Affiliation(s)
- Fernanda Sucharski
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Camila Coelho
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Leon Hardy
- Department of Physics, University of South Florida, Tampa, USA
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil.
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Džupponová V, Tomášková N, Antošová A, Sedlák E, Žoldák G. Salt-Specific Suppression of the Cold Denaturation of Thermophilic Multidomain Initiation Factor 2. Int J Mol Sci 2023; 24:ijms24076787. [PMID: 37047761 PMCID: PMC10094840 DOI: 10.3390/ijms24076787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Thermophilic proteins and enzymes are attractive for use in industrial applications due to their resistance against heat and denaturants. Here, we report on a thermophilic protein that is stable at high temperatures (Ttrs, hot 67 °C) but undergoes significant unfolding at room temperature due to cold denaturation. Little is known about the cold denaturation of thermophilic proteins, although it can significantly limit their applications. We investigated the cold denaturation of thermophilic multidomain protein translation initiation factor 2 (IF2) from Thermus thermophilus. IF2 is a GTPase that binds to ribosomal subunits and initiator fMet-tRNAfMet during the initiation of protein biosynthesis. In the presence of 9 M urea, measurements in the far-UV region by circular dichroism were used to capture details about the secondary structure of full-length IF2 protein and its domains during cold and hot denaturation. Cold denaturation can be suppressed by salt, depending on the type, due to the decreased heat capacity. Thermodynamic analysis and mathematical modeling of the denaturation process showed that salts reduce the cooperativity of denaturation of the IF2 domains, which might be associated with the high frustration between domains. This characteristic of high interdomain frustration may be the key to satisfying numerous diverse contacts with ribosomal subunits, translation factors, and tRNA.
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Affiliation(s)
- Veronika Džupponová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University, Jesenna 5, 04001 Košice, Slovakia
| | - Nataša Tomášková
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
| | - Andrea Antošová
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Košice, Slovakia
| | - Erik Sedlák
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
- Center for Interdisciplinary Biosciences, Technology and Innovation Park P.J. Šafárik University, Trieda SNP 1, 04011 Košice, Slovakia
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park P.J. Šafárik University, Trieda SNP 1, 04011 Košice, Slovakia
- Center for Interdisciplinary Biosciences, Cassovia New Industry Cluster, Trieda SNP 1, 04011 Košice, Slovakia
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35
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Devlin T, Marx DC, Roskopf MA, Bubb QR, Plummer AM, Fleming KG. FkpA enhances membrane protein folding using an extensive interaction surface. Protein Sci 2023; 32:e4592. [PMID: 36775935 PMCID: PMC10031210 DOI: 10.1002/pro.4592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/14/2023]
Abstract
Outer membrane protein (OMP) biogenesis in gram-negative bacteria is managed by a network of periplasmic chaperones that includes SurA, Skp, and FkpA. These chaperones bind unfolded OMPs (uOMPs) in dynamic conformational ensembles to suppress aggregation, facilitate diffusion across the periplasm, and enhance folding. FkpA primarily responds to heat-shock stress, but its mechanism is comparatively understudied. To determine FkpA chaperone function in the context of OMP folding, we monitored the folding of three OMPs and found that FkpA, unlike other periplasmic chaperones, increases the folded yield but decreases the folding rate of OMPs. The results indicate that FkpA behaves as a chaperone and not as a folding catalyst to influence the OMP folding trajectory. Consistent with the folding assay results, FkpA binds all three uOMPs as determined by sedimentation velocity (SV) and photo-crosslinking experiments. We determine the binding affinity between FkpA and uOmpA171 by globally fitting SV titrations and find it to be intermediate between the known affinities of Skp and SurA for uOMP clients. Notably, complex formation steeply depends on the urea concentration, suggesting an extensive binding interface. Initial characterizations of the complex using photo-crosslinking indicate that the binding interface spans the entire FkpA molecule. In contrast to prior findings, folding and binding experiments performed using subdomain constructs of FkpA demonstrate that the full-length chaperone is required for full activity. Together these results support that FkpA has a distinct and direct effect on OMP folding that it achieves by utilizing an extensive chaperone-client interface to tightly bind clients.
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Affiliation(s)
- Taylor Devlin
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Dagan C. Marx
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Michaela A. Roskopf
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Quenton R. Bubb
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Ashlee M. Plummer
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Karen G. Fleming
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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Narsimulu B, Qureshi R, Jakkula P, Singh P, Arifuddin M, Qureshi IA. Exploration of seryl tRNA synthetase to identify potent inhibitors against leishmanial parasites. Int J Biol Macromol 2023; 237:124118. [PMID: 36963547 DOI: 10.1016/j.ijbiomac.2023.124118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/26/2023]
Abstract
Aminoacyl-tRNA synthetases are crucial enzymes for cellular protein metabolism and have been considered as an attractive target for development of new antimicrobials. In the current study, seryl tRNA synthetase of Leishmania donovani (LdSerRS) and its mutants were purified and characterized through biochemical and structural methods. Purified LdSerRS was found to be enzymatically active and exhibited more alpha helices in secondary structure. The enzymatic activity of purified protein was observed as highest near physiological temperature and pH. Mutation in ATP binding residues (R295 and E297) demonstrated reduction in the affinity for cofactor with no significant deviation in secondary structure. In vitro inhibition studies with ureidosulfocoumarin derivatives helped to identify Comp 5l as a specific inhibitor for leishmanial SerRS that showed lesser potency towards purified HsSerRS. The identified compound presented competitive mode of inhibition for LdSerRS and also revealed druglikeness along with very low toxicity for human macrophages. Structural analysis of protein and ligand complex depicted the binding of Comp 5l into the cofactor binding site of LdSerRS with high affinity succeeded by validation employing molecular dynamics simulations. Altogether, our study presents a promising scaffold to explore small molecules to target the enzymatic activity of leishmanial SerRS to develop the specific therapeutics.
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Affiliation(s)
- Bandigi Narsimulu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Rahila Qureshi
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Pranay Jakkula
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Priti Singh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Mohammed Arifuddin
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India.
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37
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Clamp Interactions with +3/+6 Duplex and Upstream-to-Downstream Allosteric Effects in Late Steps of Forming a Stable RNA Polymerase-Promoter Open Complex. J Mol Biol 2023; 435:167990. [PMID: 36736885 DOI: 10.1016/j.jmb.2023.167990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Stable 37 °C open complexes (OC) of E. coli RNA polymerase (RNAP) at λPR and T7A1 promoters form at similar rates but have very different lifetimes. To understand the downstream interactions responsible for OC lifetime, how promoter sequence directs them and when they form, we report lifetimes of stable OC and unstable late (I2) intermediates for promoters with different combinations of λPR (L) and T7A1 (T) discriminators, core promoters and UP elements. I2 lifetimes are similarly short, while stable OC lifetimes differ greatly, determined largely by the discriminator and modulated by core-promoter and UP elements. The free energy change ΔG3o for I2 → stable OC is approximately -4 kcal more favorable for L-discriminator than for T-discriminator promoters. Downstream-truncation at +6 (DT+6) greatly destabilizes OC at L-discriminator but not T-discriminator promoters, making all ΔG3o values similar (approximately -4 kcal). Urea reduces OC lifetime greatly by affecting ΔG3o. We deduce that urea acts by disfavoring coupled folding of key elements of the β'-clamp, that I2 is an open-clamp OC, and that clamp-closing in I2 → stable OC involves coupled folding. Differences in ΔG3o between downstream-truncated and full-length promoters yield contributions to ΔG3o from interactions with downstream mobile elements (DME) including β-lobe and β'-jaw, more favorable for L-discriminator than for T-discriminator promoters. We deduce how competition between far-downstream DNA and σ70 region 1.1 affects ΔG3o values. We discuss variant-specific ΔG3o contributions in terms of the allosteric network by which differences in discriminator and -10 sequence are sensed and transmitted downstream to affect DME-duplex interactions in I2 → stable OC.
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38
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Collagen-like Motifs of SasG: A Novel Fold for Protein Mechanical Strength. J Mol Biol 2023; 435:167980. [PMID: 36708761 DOI: 10.1016/j.jmb.2023.167980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The Staphylococcus aureus surface protein G (SasG) is associated with host colonisation and biofilm formation. As colonisation occurs at the liquid-substrate interface bacteria are subject to a myriad of external forces and, presumably as a consequence, SasG displays extreme mechanical strength. This mechanical phenotype arises from the B-domain; a repetitive region composed of alternating E and G5 subdomains. These subdomains have an unusual structure comprising collagen-like regions capped by triple-stranded β-sheets. To identify the determinants of SasG mechanical strength, we characterised the mechanical phenotype and thermodynamic stability of 18 single substitution variants of a pseudo-wildtype protein. Visualising the mechanically-induced transition state at a residue-level by ϕ-value analysis reveals that the main force-bearing regions are the N- and C-terminal 'Mechanical Clamps' and their side-chain interactions. This is tailored by contacts at the pseudo-hydrophobic core interface. We also describe a novel mechanical motif - the collagen-like region and show that glycine to alanine substitutions, analogous to those found in Osteogenesis Imperfecta (brittle bone disease), result in a significantly reduced mechanical strength.
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39
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Seelig J, Seelig A. Protein Unfolding—Thermodynamic Perspectives and Unfolding Models. Int J Mol Sci 2023; 24:ijms24065457. [PMID: 36982534 PMCID: PMC10049513 DOI: 10.3390/ijms24065457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/14/2023] Open
Abstract
We review the key steps leading to an improved analysis of thermal protein unfolding. Thermal unfolding is a dynamic cooperative process with many short-lived intermediates. Protein unfolding has been measured by various spectroscopic techniques that reveal structural changes, and by differential scanning calorimetry (DSC) that provides the heat capacity change Cp(T). The corresponding temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) have thus far been evaluated using a chemical equilibrium two-state model. Taking a different approach, we demonstrated that the temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) can be obtained directly by a numerical integration of the heat capacity profile Cp(T). DSC thus offers the unique possibility to assess these parameters without resorting to a model. These experimental parameters now allow us to examine the predictions of different unfolding models. The standard two-state model fits the experimental heat capacity peak quite well. However, neither the enthalpy nor entropy profiles (predicted to be almost linear) are congruent with the measured sigmoidal temperature profiles, nor is the parabolic free energy profile congruent with the experimentally observed trapezoidal temperature profile. We introduce three new models, an empirical two-state model, a statistical–mechanical two-state model and a cooperative statistical-mechanical multistate model. The empirical model partially corrects for the deficits of the standard model. However, only the two statistical–mechanical models are thermodynamically consistent. The two-state models yield good fits for the enthalpy, entropy and free energy of unfolding of small proteins. The cooperative statistical–mechanical multistate model yields perfect fits, even for the unfolding of large proteins such as antibodies.
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40
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Thurlkill RL, Trevino SR, Scholtz JM, Grimsley GR. Determining the Conformational Stability of a Protein from Urea and Thermal Unfolding Curves. Curr Protoc 2023; 3:e723. [PMID: 36952496 DOI: 10.1002/cpz1.723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
This article contains protocols for determining the conformational stability of a globular protein from either urea or thermal unfolding curves. Circular dichroism is the optical spectroscopic technique most commonly used to monitor protein unfolding. These protocols describe how to analyze data from an unfolding curve to obtain the thermodynamic parameters necessary to calculate conformational stability, and how to determine differences in stability between protein variants. Curr. Protoc. Protein Sci. 71:28.4.1-28.4.14. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Determining protein conformational stability from urea-induced unfolding curves Support Protocol 1: Preparing a urea stock solution Support Protocol 2: Analyzing urea unfolding curves Basic Protocol 2: Determining the conformational stability of a protein from thermal unfolding curves Support Protocol 3: Analyzing thermal unfolding curves Support Protocol 4: Determining differences in conformational stability for protein variants.
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Affiliation(s)
- Richard L Thurlkill
- Department of Chemistry and Physics, Louisiana Tech University, Ruston, Louisiana
| | - Saul R Trevino
- College of Science and Engineering, Houston Christian University, Houston, Texas
| | - J Martin Scholtz
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, Iowa
| | - Gerald R Grimsley
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas
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41
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Dixit A, Chakraborty A, Nath JR, Chowdhury PK, Kundu B. Ocular protein optineurin shows reversibility from unfolded states and exhibits chaperone-like activity. RSC Adv 2023; 13:6827-6837. [PMID: 36865578 PMCID: PMC9972007 DOI: 10.1039/d2ra07931c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/16/2023] [Indexed: 03/04/2023] Open
Abstract
Optineurin (OPTN) is a multifunctional, ubiquitously expressed cytoplasmic protein, mutants of which are associated with primary open-angle glaucoma (POAG) and amyotrophic lateral sclerosis (ALS). The most abundant heat shock protein crystallin, known for its remarkable thermodynamic stability and chaperoning activity, allows ocular tissues to withstand stress. The presence of OPTN in ocular tissues is intriguing. Interestingly, OPTN also harbors heat shock elements in its promoter region. Sequence analysis of OPTN exhibits intrinsically disordered regions and nucleic acid binding domains. These properties hinted that OPTN might be endowed with sufficient thermodynamic stability and chaperoning activity. However, these attributes of OPTN have not yet been explored. Here, we studied these properties through thermal and chemical denaturation experiments and monitored the processes using CD, fluorimetry, differential scanning calorimetry, and dynamic light scattering. We found that upon heating, OPTN reversibly forms higher-order multimers. OPTN also displayed a chaperone-like function by reducing the thermal aggregation of bovine carbonic anhydrase. It regains its native secondary structure, RNA-binding property, and melting temperature (T m) after refolding from a thermally as well as chemically denatured state. From our data, we conclude that OPTN, with its unique ability to revert from the stress-mediated unfolded state and its unique chaperoning function, is a valuable protein of the ocular tissues.
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Affiliation(s)
- Anjali Dixit
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi India
| | - Ankan Chakraborty
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi India
| | - Jyoti Rani Nath
- Department of Chemistry, Indian Institute of TechnologyDelhiIndia
| | | | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi India
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42
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Rivera M, Mjaavatten A, Smith SB, Baez M, Wilson CAM. Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers. Biophys J 2023; 122:513-521. [PMID: 36587240 PMCID: PMC9941719 DOI: 10.1016/j.bpj.2022.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
Temperature is a useful system variable to gather kinetic and thermodynamic information from proteins. Usually, free energy and the associated entropic and enthalpic contributions are obtained by quantifying the conformational equilibrium based on melting experiments performed in bulk conditions. Such experiments are suitable only for those small single-domain proteins whose side reactions of irreversible aggregation are unlikely to occur. Here, we avoid aggregation by pulling single-protein molecules in a thermo-regulated optical tweezers. Thus, we are able to explore the temperature dependence of the thermodynamic and kinetic parameters of MJ0366 from Methanocaldococcus jannaschii at the single-molecule level. By performing force-ramp experiments between 2°C and 40°C, we found that MJ0366 has a nonlinear dependence of free energy with temperature and a specific heat change of 2.3 ± 1.2 kcal/mol∗K. These thermodynamic parameters are compatible with a two-state unfolding/refolding mechanism for MJ0366. However, the kinetics measured as a function of the temperature show a complex behavior, suggesting a three-state folding mechanism comprising a high-energy intermediate state. The combination of two perturbations, temperature and force, reveals a high-energy species in the folding mechanism of MJ0366 not detected in force-ramp experiments at constant temperature.
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Affiliation(s)
- Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | | | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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Santorelli D, Marcocci L, Pennacchietti V, Nardella C, Diop A, Pietrangeli P, Pagano L, Toto A, Malagrinò F, Gianni S. Understanding the molecular basis of folding cooperativity through a comparative analysis of a multidomain protein and its isolated domains. J Biol Chem 2023; 299:102983. [PMID: 36739950 PMCID: PMC10017356 DOI: 10.1016/j.jbc.2023.102983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023] Open
Abstract
Although cooperativity is a well-established and general property of folding, our current understanding of this feature in multidomain folding is still relatively limited. In fact, there are contrasting results indicating that the constituent domains of a multidomain protein may either fold independently on each other or exhibit interdependent supradomain phenomena. To address this issue, here we present the comparative analysis of the folding of a tandem repeat protein, comprising two contiguous PDZ domains, in comparison to that of its isolated constituent domains. By analyzing in detail the equilibrium and kinetics of folding at different experimental conditions, we demonstrate that despite each of the PDZ domains in isolation being capable of independent folding, at variance with previously characterized PDZ tandem repeats, the full-length construct folds and unfolds as a single cooperative unit. By exploiting quantitatively, the comparison of the folding of the tandem repeat to those observed for its constituent domains, as well as by characterizing a truncated variant lacking a short autoinhibitory segment, we successfully rationalize the molecular basis of the observed cooperativity and attempt to infer some general conclusions for multidomain systems.
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Affiliation(s)
- Daniele Santorelli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Lucia Marcocci
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Awa Diop
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Paola Pietrangeli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Livia Pagano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Francesca Malagrinò
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Naples, Italy.
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy.
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44
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Wu T, Yu JC, Suresh A, Gale-Day ZJ, Alteen MG, Woo AS, Millbern Z, Johnson OT, Carroll EC, Partch CL, Fourches D, Vinueza NR, Vocadlo DJ, Gestwicki JE. Conformationally responsive dyes enable protein-adaptive differential scanning fluorimetry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525251. [PMID: 36747624 PMCID: PMC9900766 DOI: 10.1101/2023.01.23.525251] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Flexible in vitro methods alter the course of biological discoveries. Differential Scanning Fluorimetry (DSF) is a particularly versatile technique which reports protein thermal unfolding via fluorogenic dye. However, applications of DSF are limited by widespread protein incompatibilities with the available DSF dyes. Here, we enable DSF applications for 66 of 70 tested proteins (94%) including 10 from the SARS-CoV2 virus using a chemically diverse dye library, Aurora, to identify compatible dye-protein pairs in high throughput. We find that this protein-adaptive DSF platform (paDSF) not only triples the previous protein compatibility, but also fundamentally extends the processes observable by DSF, including interdomain allostery in O-GlcNAc Transferase (OGT). paDSF enables routine measurement of protein stability, dynamics, and ligand binding.
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Affiliation(s)
- Taiasean Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco; San Francisco, CA, 94038, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco; San Francisco, CA, 94038, USA
| | - Joshua C. Yu
- Department of Pharmaceutical Chemistry, University of California San Francisco; San Francisco, CA, 94038, USA
| | - Arundhati Suresh
- Department of Pharmaceutical Chemistry, University of California San Francisco; San Francisco, CA, 94038, USA
| | - Zachary J. Gale-Day
- Department of Pharmaceutical Chemistry, University of California San Francisco; San Francisco, CA, 94038, USA
| | - Matthew G. Alteen
- Department of Chemistry, Simon Fraser University; Burnaby, BC V5A 1S6, Canada
| | - Amanda S. Woo
- Department of Pharmaceutical Chemistry, University of California San Francisco; San Francisco, CA, 94038, USA
| | - Zoe Millbern
- Department of Textile Engineering, North Carolina State University; Raleigh, NC 27695, USA
| | - Oleta T. Johnson
- Institute for Neurodegenerative Diseases, University of California, San Francisco; San Francisco, CA, 94038, USA
| | - Emma C. Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco; San Francisco, CA, 94038, USA
| | - Carrie L. Partch
- Department of Chemistry, University of California, Santa Cruz; Santa Cruz, CA, 95064, USA
| | - Denis Fourches
- Department of Textile Engineering, North Carolina State University; Raleigh, NC 27695, USA
| | - Nelson R. Vinueza
- Department of Textile Engineering, North Carolina State University; Raleigh, NC 27695, USA
| | - David J. Vocadlo
- Department of Chemistry, Simon Fraser University; Burnaby, BC V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University; Burnaby, BC V5A 1S6, Canada
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco; San Francisco, CA, 94038, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco; San Francisco, CA, 94038, USA
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Smith CA, Sonneson GJ, Hoey RJ, Hinerman JM, Sheehy K, Walter R, Herr AB, Horn JR. Molecular recognition requires dimerization of a VHH antibody. MAbs 2023; 15:2215363. [PMID: 37243579 PMCID: PMC10228392 DOI: 10.1080/19420862.2023.2215363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023] Open
Abstract
Camelid heavy-chain-only antibodies are a unique class of antibody that possesses only a single variable domain (termed VHH) for antigen recognition. Despite their apparent canonical mechanism of target recognition, where a single VHH domain binds a single target, an anti-caffeine VHH has been observed to possess 2:1 stoichiometry. Here, the structure of the anti-caffeine VHH/caffeine complex enabled the generation and biophysical analysis of variants that were used to better understand the role of VHH homodimerization in caffeine recognition. VHH interface mutants and caffeine analogs, which were examined to probe the mechanism of caffeine binding, suggested caffeine recognition is only possible with the VHH dimer species. Correspondingly, in the absence of caffeine, the anti-caffeine VHH was found to form a dimer with a dimerization constant comparable to that observed with VH:VL domains in conventional antibody systems, which was most stable near physiological temperature. While the VHH:VHH dimer structure (at 1.13 Å resolution) is reminiscent of conventional VH:VL heterodimers, the homodimeric VHH possesses a smaller angle of domain interaction, as well as a larger amount of apolar surface area burial. To test the general hypothesis that the short complementarity-determining region-3 (CDR3) may help drive VHH:VHH homodimerization, an anti-picloram VHH domain containing a short CDR3 was generated and characterized, which revealed it also existed as dimer species in solution. These results suggest homodimer-driven recognition may represent a more common method of VHH ligand recognition, opening opportunities for novel VHH homodimer affinity reagents and helping to guide their use in chemically induced dimerization applications.
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Affiliation(s)
- Christopher A. Smith
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Gregory J. Sonneson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Robert J. Hoey
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Jennifer M. Hinerman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Kimberly Sheehy
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Richard Walter
- Shamrock Structures, LLC, Woodridge, IL, USA
- Joliet XTALPAC LLC, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - James R. Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
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Félix SS, Laurents DV, Oroz J, Cabrita EJ. Fused in sarcoma undergoes cold denaturation: Implications for phase separation. Protein Sci 2023; 32:e4521. [PMID: 36453011 PMCID: PMC9793971 DOI: 10.1002/pro.4521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The mediation of liquid-liquid phase separation (LLPS) for fused in sarcoma (FUS) protein is generally attributed to the low-complexity, disordered domains and is enhanced at low temperature. The role of FUS folded domains on the LLPS process remains relatively unknown since most studies are mainly based on fragmented FUS domains. Here, we investigate the effect of metabolites on full-length (FL) FUS LLPS using turbidity assays and differential interference contrast (DIC) microscopy, and explore the behavior of the folded domains by nuclear magnetic resonance (NMR) spectroscopy. FL FUS LLPS is maximal at low concentrations of glucose and glutamate, moderate concentrations of NaCl, Zn2+ , and Ca2+ and at the isoelectric pH. The FUS RNA recognition motif (RRM) and zinc-finger (ZnF) domains are found to undergo cold denaturation above 0°C at a temperature that is determined by the conformational stability of the ZnF domain. Cold unfolding exposes buried nonpolar residues that can participate in LLPS-promoting hydrophobic interactions. Therefore, these findings constitute the first evidence that FUS globular domains may have an active role in LLPS under cold stress conditions and in the assembly of stress granules, providing further insight into the environmental regulation of LLPS.
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Affiliation(s)
- Sara S. Félix
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | | | - Javier Oroz
- Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | - Eurico J. Cabrita
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal
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47
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Negi I, Jangra R, Gharu A, Trant JF, Sharma P. Guanidinium–amino acid hydrogen-bonding interactions in protein crystal structures: implications for guanidinium-induced protein denaturation. Phys Chem Chem Phys 2023; 25:857-869. [DOI: 10.1039/d2cp04943k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structural analysis of guanidinium–amino acid interaction pairs in protein crystal structures is coupled with an effective scheme for classifying the optimized pairs, to gain understanding of the guanidinium:protein hydrogen bonding modes.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Raman Jangra
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Amit Gharu
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - John F. Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave. Windsor ON, N9B 3P4, Canada
- Binary Star Research Services, LaSalle, ON, N9J 3 X 8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave. Windsor ON, N9B 3P4, Canada
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48
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Hollås H, Ramirez J, Nominé Y, Kostmann C, Toto A, Gianni S, Travé G, Vedeler A. The cooperative folding of annexin A2 relies on a transient nonnative intermediate. Biophys J 2022; 121:4492-4504. [PMID: 36325614 PMCID: PMC9748365 DOI: 10.1016/j.bpj.2022.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/29/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Annexins (Anxs) are a family of highly homologous proteins that bind and aggregate lipid vesicles in the presence of calcium. All members of the family contain a variable N-terminus determining specific functions, followed by a conserved core region responsible for the general calcium-dependent lipid-binding property. The core structure consists of four homologous domains (DI-DIV), each consisting of a right-handed super-helix of five α-helices. We present data from a combination of site-directed mutagenesis, NMR, and circular dichroism showing that the G25-D34 region of the N-terminus as well as the contacts between residues D38A, R63A, and Q67A of AnxA2-DI are crucial for the autonomous folding and stability of DI of AnxA2. However, we also show that the folding of the full-length protein is very robust in that mutations and truncations that disrupted the folding of AnxA2-DI did not abolish the folding of full-length AnxA2, only lowering its thermal stability. This robustness of the folding of full-length AnxA2 is likely to be mediated by the existence of at least one transient nonnative intermediate as suggested by our kinetic data using stopped-flow fluorescence experiments. We also show that hydrophobic amino acids in AnxA2-DI involved in interfacial contacts with AnxA2-DIV are important for the cooperative folding and stability of the full-length protein. Mutating all of the V57E-V98R-G101Y residues in AnxA2-DI did not affect the folding of the domain, only its stability, but prevented the cooperative folding of the full-length protein. Our collective results favor a highly cooperative and robust folding process mediated by alternative intermediate steps. Since AnxA2 is a multifunctional protein involved in several steps of the progression of cell transformation, these data on structure and folding pathways are therefore crucial to designing anticancer drugs targeting AnxA2.
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Affiliation(s)
- Hanne Hollås
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Juan Ramirez
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Yves Nominé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Camille Kostmann
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Angelo Toto
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Stefano Gianni
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Gilles Travé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France.
| | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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Recombinant Globular Domain of TcpA Pilin from Vibrio cholerae El Tor: Recovery from Inclusion Bodies and Structural Characterization. Life (Basel) 2022; 12:life12111802. [DOI: 10.3390/life12111802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The production of recombinant proteins in Escherichia coli cells is often hampered by aggregation of newly synthesized proteins and formation of inclusion bodies. Here we propose the use of transverse urea gradient electrophoresis (TUGE) in testing the capability of folding of a recombinant protein from inclusion bodies dissolved in urea. A plasmid encoding the amino acid sequence 55–224 of TcpA pilin (C-terminal globular domain: TcpA-C) from Vibrio cholerae El Tor enlarged by a His-tag on its N-terminus was expressed in E. coli cells. The major fraction (about 90%) of the target polypeptide was detected in cell debris. The polypeptide was isolated from the soluble fraction and recovered from inclusion bodies after their urea treatment. Some structural properties of the polypeptide from each sample proved identical. The refolding protocol was developed on the basis of TUGE data and successfully used for the protein large-scale recovery from inclusion bodies. Spectral, hydrodynamic, and thermodynamic characteristics of the recombinant TcpA recovered from inclusion bodies indicate the presence of a globular conformation with a pronounced secondary structure and a rigid tertiary structure, which is promising for the design of immunodiagnostics preparations aimed to assess the pilin level in different strains of V. cholerae and to develop cholera vaccines.
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50
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Esperante S, Alvarez-Paggi D, Salgueiro M, Desimone M, de Oliveira G, Arán M, García-Pardo J, Aptekmann A, Ventura S, Alonso L, de Prat-Gay G. A finely tuned interplay between calcium binding, ionic strength and pH modulates conformational and oligomerization equilibria in the Respiratory Syncytial Virus Matrix (M) protein. Arch Biochem Biophys 2022; 731:109424. [DOI: 10.1016/j.abb.2022.109424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/29/2022] [Indexed: 11/30/2022]
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