1
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Lin Y, Horne WS. Backbone Modification in a Protein Hydrophobic Core. Chemistry 2024; 30:e202401890. [PMID: 38753977 PMCID: PMC11345847 DOI: 10.1002/chem.202401890] [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: 05/15/2024] [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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2
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Petrovicz VL, Pasztuhov I, Martinek TA, Hegedüs Z. Site-directed allostery perturbation to probe the negative regulation of hypoxia inducible factor-1α. RSC Chem Biol 2024; 5:711-720. [PMID: 39092442 PMCID: PMC11289882 DOI: 10.1039/d4cb00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/27/2024] [Indexed: 08/04/2024] Open
Abstract
The interaction between the intrinsically disordered transcription factor HIF-1α and the coactivator proteins p300/CBP is essential in the fast response to low oxygenation. The negative feedback regulator, CITED2, switches off the hypoxic response through a very efficient irreversible mechanism. The negative cooperativity with HIF-1α relies on the formation of a ternary intermediate that leads to allosteric structural changes in p300/CBP, in which the cooperative folding/binding of the CITED2 sequence motifs plays a key role. Understanding the contribution of a binding motif to the structural changes in relation to competition efficiency provides invaluable insights into the molecular mechanism. Our strategy is to site-directedly perturb the p300-CITED2 complex's structure without significantly affecting binding thermodynamics. In this way, the contribution of a sequence motif to the negative cooperativity with HIF-1α would mainly depend on the induced structural changes, and to a lesser extent on binding affinity. Using biophysical assays and NMR measurements, we show here that the interplay between the N-terminal tail and the rest of the binding motifs of CITED2 is crucial for the unidirectional displacement of HIF-1α. We introduce an advantageous approach for evaluating the roles of the different sequence parts with the help of motif-by-motif backbone perturbations.
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Affiliation(s)
- Vencel L Petrovicz
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - István Pasztuhov
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - Tamás A Martinek
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
- HUN-REN SZTE Biomimetic Systems Research Group 8 Dóm tér Szeged 6720 Hungary
| | - Zsófia Hegedüs
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
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3
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Santhouse JR, Leung JMG, Chong LT, Horne WS. Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein. Chem Sci 2024; 15:675-682. [PMID: 38179541 PMCID: PMC10763558 DOI: 10.1039/d3sc03976e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024] Open
Abstract
Sequence-encoded protein folding is a ubiquitous biological process that has been successfully engineered in a range of oligomeric molecules with artificial backbone chemical connectivity. A remarkable aspect of protein folding is the contrast between the rapid rates at which most sequences in nature fold and the vast number of conformational states possible in an unfolded chain with hundreds of rotatable bonds. Research efforts spanning several decades have sought to elucidate the fundamental chemical principles that dictate the speed and mechanism of natural protein folding. In contrast, little is known about how protein mimetic entities transition between an unfolded and folded state. Here, we report effects of altered backbone connectivity on the folding kinetics and mechanism of the B domain of Staphylococcal protein A (BdpA), an ultrafast-folding sequence. A combination of experimental biophysical analysis and atomistic molecular dynamics simulations performed on the prototype protein and several heterogeneous-backbone variants reveal the interplay among backbone flexibility, folding rates, and structural details of the transition state ensemble. Collectively, these findings suggest a significant degree of plasticity in the mechanisms that can give rise to ultrafast folding in the BdpA sequence and provide atomic level insights into how protein mimetic chains adopt an ordered folded state.
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Affiliation(s)
| | - Jeremy M G Leung
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
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4
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Rao SR, Harmon TW, Heath SL, Wolfe JA, Santhouse JR, O'Brien GL, Distefano AN, Reinert ZE, Horne WS. Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States. Pept Sci (Hoboken) 2023; 115:e24297. [PMID: 37397503 PMCID: PMC10312354 DOI: 10.1002/pep2.24297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 03/03/2024]
Abstract
The construction of protein-sized synthetic chains that blend natural amino acids with artificial monomers to create so-called heterogeneous-backbones is a powerful approach to generate complex folds and functions from bio-inspired agents. A variety of techniques from structural biology commonly used to study natural proteins have been adapted to investigate folding in these entities. In NMR characterization of proteins, proton chemical shift is a straightforward to acquire, information-rich metric that bears directly on a variety of properties related to folding. Leveraging chemical shift to gain insight into folding requires a set of reference chemical shift values corresponding to each building block type (i.e., the 20 canonical amino acids in the case of natural proteins) in a random coil state and knowledge of systematic changes in chemical shift associated with particular folded conformations. Although well documented for natural proteins, these issues remain unexplored in the context of protein mimetics. Here, we report random coil chemical shift values for a library of artificial amino acid monomers frequently used to construct heterogeneous-backbone protein analogues as well as a spectroscopic signature associated with one monomer class, β3-residues bearing proteinogenic side chains, adopting a helical folded conformation. Collectively, these results will facilitate the continued utilization of NMR for the study of structure and dynamics in protein-like artificial backbones.
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Affiliation(s)
- Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Thomas W Harmon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Shelby L Heath
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jacob A Wolfe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | | | - Gregory L O'Brien
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexis N Distefano
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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5
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Santhouse JR, Leung JMG, Chong LT, Horne WS. Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics. Chem Sci 2022; 13:11798-11806. [PMID: 36320921 PMCID: PMC9580521 DOI: 10.1039/d2sc04427g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/19/2022] [Indexed: 12/28/2022] Open
Abstract
Sequence-encoded folding is the foundation of protein structure and is also possible in synthetic chains of artificial chemical composition. In natural proteins, the characteristics of the unfolded state are as important as those of the folded state in determining folding energetics. While much is known about folded structures adopted by artificial protein-like chains, corresponding information about the unfolded states of these molecules is lacking. Here, we report the consequences of altered backbone composition on the structure, stability, and dynamics of the folded and unfolded states of a compact helix-rich protein. Characterization through a combination of biophysical experiments and atomistic simulation reveals effects of backbone modification that depend on both the type of artificial monomers employed and where they are applied in sequence. In general, introducing artificial connectivity in a way that reinforces characteristics of the unfolded state ensemble of the prototype natural protein minimizes the impact of chemical changes on folded stability. These findings have implications in the design of protein mimetics and provide an atomically detailed picture of the unfolded state of a natural protein and artificial analogues under non-denaturing conditions. Biophysical experiments and atomistic simulation reveal impacts of protein backbone alteration on the ensemble that defines the unfolded state. These effects have implications on folded stability of protein mimetics.![]()
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Affiliation(s)
| | - Jeremy M. G. Leung
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15211, USA
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15211, USA
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15211, USA
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6
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Bejger M, Fortuna P, Drewniak-Switalska M, Plewka J, Rypniewski W, Berlicki Ł. A computationally designed β-amino acid-containing miniprotein. Chem Commun (Camb) 2021; 57:6015-6018. [PMID: 34032224 DOI: 10.1039/d1cc02192c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new miniprotein built from three helices, including one structure based on the ααβαααβ sequence pattern was developed. Its crystal structure revealed a compact conformation with a well-packed hydrophobic core of unprecedented structure. The miniprotein formed dimers that were stabilized by the interaction of their hydrophobic surfaces.
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Affiliation(s)
- Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland
| | - Paulina Fortuna
- Department of Bioorganic Chemistry Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland. and Department of Medical Biochemistry, Wrocław Medical University, Pausteura 1, Wroclaw 50-368, Poland
| | - Magda Drewniak-Switalska
- Department of Bioorganic Chemistry Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland.
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian Univeristy, Gronostajowa 2, Kraków 30-387, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland.
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7
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Drewniak-Świtalska M, Barycza B, Rudzińska-Szostak E, Morawiak P, Berlicki Ł. Constrained beta-amino acid-containing miniproteins. Org Biomol Chem 2021; 19:4272-4278. [PMID: 34010377 DOI: 10.1039/d1ob00309g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
The construction of β-amino acid-containing peptides that fold to tertiary structures in solution remains challenging. Two model miniproteins, namely, Trp-cage and FSD, were scanned using a constrained β-amino acid in order to evaluate its impact on the folding process. Relationships between forces stabilizing the miniprotein structure and conformational stability of analogues were found. The possibility of a significant increase of the conformational stability of the studied miniproteins by substitution with the β-amino acid at the terminus of a helix is shown. On the basis of these results, β-amino acid containing-peptide analogs with helical fragments substantially altered by the incorporation of several constrained β-amino acids were designed, synthesized and evaluated with respect to their structure and stability. The smallest known β-amino acid-containing peptide with a well-defined tertiary structure is described.
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Affiliation(s)
- Magda Drewniak-Świtalska
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Barbara Barycza
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Paweł Morawiak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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8
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Santhouse JR, Rao SR, Horne WS. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Methods Enzymol 2021; 656:93-122. [PMID: 34325801 PMCID: PMC8392274 DOI: 10.1016/bs.mie.2021.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent years have seen a growing number of examples of designed oligomeric molecules with artificial backbone connectivity that are capable of adopting complex folded tertiary structures analogous to those seen in natural proteins. A range of experimental techniques from structural biology and biophysics have been brought to bear in the study of these proteomimetic agents. Here, we discuss some considerations encountered in the characterization of high-resolution folded structure as well as folding thermodynamics of protein-like artificial backbones. We provide an overview of the use of X-ray crystallography and NMR spectroscopy in such systems and review example applications of these methods in the primary literature. Further, we provide detailed protocols for two experiments that have proved useful in our prior and ongoing efforts to compare folding thermodynamics between natural protein domains and heterogeneous-backbone counterparts.
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Affiliation(s)
| | - Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
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9
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Ożga K, Drewniak-Świtalska M, Rudzińska-Szostak E, Berlicki Ł. Towards Foldameric Miniproteins: A Helix-Turn-Helix Motif. Chempluschem 2021; 86:646-649. [PMID: 33856118 DOI: 10.1002/cplu.202100090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Indexed: 11/11/2022]
Abstract
Numerous beta-amino acid containing peptides forming secondary structures have been already described, however the design of higher-order structures remains poorly explored. The methodology allowing construction of sequence patterns containing few rigid secondary element was proposed and experimentally validated. On the basis of 9/10/9/12-helix containing cis-2-aminocyclopentanecarboxylic acid (cis-ACPC) residues arranged in an ααββ sequence pattern, a conformationally stable helix-turn-helix structure was designed. The connection between two helices was also constructed using cis-ACPC residues. Five examples of designed peptides were obtained and analyzed using circular dichroism and nuclear magnetic resonance spectroscopy, which confirmed the assumed way of folding. The NMR structure was calculated for the peptide with the highest number of non-sequential contacts.
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Affiliation(s)
- Katarzyna Ożga
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Magda Drewniak-Świtalska
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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10
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Ginn HM. Vagabond: bond-based parametrization reduces overfitting for refinement of proteins. Acta Crystallogr D Struct Biol 2021; 77:424-437. [PMID: 33825703 PMCID: PMC8025884 DOI: 10.1107/s2059798321000826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/24/2021] [Indexed: 11/10/2022] Open
Abstract
Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.
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Affiliation(s)
- Helen M. Ginn
- Division of Life Sciences, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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11
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Tököli A, Mag B, Bartus É, Wéber E, Szakonyi G, Simon MA, Czibula Á, Monostori É, Nyitray L, Martinek TA. Proteomimetic surface fragments distinguish targets by function. Chem Sci 2020; 11:10390-10398. [PMID: 34094300 PMCID: PMC8162404 DOI: 10.1039/d0sc03525d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/09/2020] [Indexed: 11/21/2022] Open
Abstract
The fragment-centric design promises a means to develop complex xenobiotic protein surface mimetics, but it is challenging to find locally biomimetic structures. To address this issue, foldameric local surface mimetic (LSM) libraries were constructed. Protein affinity patterns, ligand promiscuity and protein druggability were evaluated using pull-down data for targets with various interaction tendencies and levels of homology. LSM probes based on H14 helices exhibited sufficient binding affinities for the detection of both orthosteric and non-orthosteric spots, and overall binding tendencies correlated with the magnitude of the target interactome. Binding was driven by two proteinogenic side chains and LSM probes could distinguish structurally similar proteins with different functions, indicating limited promiscuity. Binding patterns displayed similar side chain enrichment values to those for native protein-protein interfaces implying locally biomimetic behavior. These analyses suggest that in a fragment-centric approach foldameric LSMs can serve as useful probes and building blocks for undruggable protein interfaces.
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Affiliation(s)
- Attila Tököli
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Beáta Mag
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Éva Bartus
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, University of Szeged Somogyi u. 4. H6720 Szeged Hungary
| | - Márton A Simon
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Ágnes Czibula
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - Éva Monostori
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
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12
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Bogetti AT, Piston HE, Leung JMG, Cabalteja CC, Yang DT, DeGrave AJ, Debiec KT, Cerutti DS, Case DA, Horne WS, Chong LT. A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics. J Chem Phys 2020; 153:064101. [PMID: 35287464 PMCID: PMC7419161 DOI: 10.1063/5.0019054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/19/2020] [Indexed: 12/17/2022] Open
Abstract
We present a new force field, AMBER ff15ipq-m, for simulations of protein mimetics in applications from therapeutics to biomaterials. This force field is an expansion of the AMBER ff15ipq force field that was developed for canonical proteins and enables the modeling of four classes of artificial backbone units that are commonly used alongside natural α residues in blended or "heterogeneous" backbones: chirality-reversed D-α-residues, the Cα-methylated α-residue Aib, homologated β-residues (β3) bearing proteinogenic side chains, and two cyclic β residues (βcyc; APC and ACPC). The ff15ipq-m force field includes 472 unique atomic charges and 148 unique torsion terms. Consistent with the AMBER IPolQ lineage of force fields, the charges were derived using the Implicitly Polarized Charge (IPolQ) scheme in the presence of explicit solvent. To our knowledge, no general force field reported to date models the combination of artificial building blocks examined here. In addition, we have derived Karplus coefficients for the calculation of backbone amide J-coupling constants for β3Ala and ACPC β residues. The AMBER ff15ipq-m force field reproduces experimentally observed J-coupling constants in simple tetrapeptides and maintains the expected conformational propensities in reported structures of proteins/peptides containing the artificial building blocks of interest-all on the μs timescale. These encouraging results demonstrate the power and robustness of the IPolQ lineage of force fields in modeling the structure and dynamics of natural proteins as well as mimetics with protein-inspired artificial backbones in atomic detail.
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Affiliation(s)
- Anthony T. Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Hannah E. Piston
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Jeremy M. G. Leung
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Darian T. Yang
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, Pennsylvania 15260, USA
| | - Alex J. DeGrave
- School of Computer Science and Engineering, University of Washington, Seattle, Washington 98115, USA
| | | | - David S. Cerutti
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 008854, USA
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 008854, USA
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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13
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Rao SR, Horne WS. Proteomimetic Zinc Finger Domains with Modified Metal-binding β-Turns. Pept Sci (Hoboken) 2020; 112. [PMID: 33733039 DOI: 10.1002/pep2.24177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mimicry of protein tertiary folds by chains artificial in backbone chemical composition leads to proteomimetic analogues with potential utility as bioactive agents and as tools to shed light on biomacromolecule behavior. Notable successes toward such molecules have been achieved; however, as protein structural diversity is vast, design principles must be continually honed as they are applied to new prototype folding patterns. One specific structure where a gap remains in understanding how to effectively generate modified backbone analogues is the metal-binding β-turn found in zinc finger domains. Literature precedent suggests several factors that may act in concert, including the artificial moiety used to modify the turn, the sequence in which it is applied, and modifications present elsewhere in the domain. Here, we report efforts to gain insights into these issues and leverage these insights to construct a zinc finger mimetic with backbone modifications throughout its constituent secondary structures. We first conduct a systematic comparison of four turn mimetics in a common host sequence, quantifying relative efficacy for use in a metal-binding context. We go on to construct a proteomimetic zinc finger domain in which the helix, strands, and turn are simultaneously modified, resulting in a variant with 23% artificial residues, a tertiary fold indistinguishable from the prototype, and a folded stability comparable to the natural backbone on which the variant is based. Collectively, the results reported provide new insights into the effects of backbone modification on structure and stability of metal-binding domains and help inform the design of metalloprotein mimetics.
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Affiliation(s)
- Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
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14
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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15
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Andrei SA, Thijssen V, Brunsveld L, Ottmann C, Milroy LG. A study on the effect of synthetic α-to-β 3-amino acid mutations on the binding of phosphopeptides to 14-3-3 proteins. Chem Commun (Camb) 2020; 55:14809-14812. [PMID: 31763628 DOI: 10.1039/c9cc07982c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Here we describe the synthesis of a series of α,β-phosphopeptides, based on the phosphoepitope site on YAP1 (yes-associated protein 1), and the biochemical, biophysical and structural characterization of their binding to 14-3-3 proteins. The impact of systematic mono- and di-substitution of α → β3 amino acid residues around the phosphoserine residue are discussed. Our results confirm the important role played by the +2 proline residue in the thermodynamics and structure of the phosphoepitope/14-3-3 interaction.
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Affiliation(s)
- Sebastian A Andrei
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.
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16
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Cary BP, Hager MV, Gellman SH. Impact of Substitution Registry on the Receptor-Activation Profiles of Backbone-Modified Glucagon-like Peptide-1 Analogues. Chembiochem 2019; 20:2834-2840. [PMID: 31172641 PMCID: PMC6861653 DOI: 10.1002/cbic.201900300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Indexed: 12/20/2022]
Abstract
Family B G protein-coupled receptors play important physiological roles and possess large extracellular domains (ECDs) that aid in binding the long polypeptide hormones that are their natural agonists. We have previously shown that agonist analogues in which subsets of native α-amino acid residues are replaced with β-amino acid residues can retain activity while avoiding proteolytic degradation. This study focuses on eight new α/β analogues of glucagon-like peptide 1 (GLP-1) that each contain five α-to-β replacements in the C-terminal half of the peptide. This portion of GLP-1 is known to adopt an α-helical conformation and contact the ECD. All four registries of the αααβ backbone pattern were evaluated; previous work has shown that the αααβ pattern supports adoption of an α-helix-like conformation. Two α-to-β replacement formats were employed, one involving β3 homologues of the native residues replaced and the other involving a cyclic β residue. GLP-1R response was characterized in terms of stimulation of cAMP production and β-arrestin recruitment. Some of the backbone-modified GLP-1 analogues display biased agonism of the GLP-1R. This study helps to establish the scope of the α→β backbone modification strategy.
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Affiliation(s)
- Brian P. Cary
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 United States
| | - Marlies V. Hager
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 United States
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17
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Conibear AC, Muttenthaler M. Advancing the Frontiers of Chemical Protein Synthesis-The 7 th CPS Meeting, Haifa, Israel. Cell Chem Biol 2019; 25:247-254. [PMID: 29547714 DOI: 10.1016/j.chembiol.2018.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The 7th Chemical Protein Synthesis Meeting took place in September 2017 in Haifa, Israel, bringing together 100 scientists from 11 countries. The cutting-edge scientific program included new synthetic strategies and ligation auxiliaries, novel insights into protein signaling and post-translational modifications, and a range of promising therapeutic applications.
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Affiliation(s)
- Anne C Conibear
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, 4072 Brisbane, Australia.
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18
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Olajos G, Hetényi A, Wéber E, Szögi T, Fülöp L, Martinek TA. Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches. Org Biomol Chem 2019; 16:5492-5499. [PMID: 30024580 DOI: 10.1039/c8ob01322e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Engineering water-soluble stand-alone β-sandwich mimetics is a current challenge because of the difficulties associated with tailoring long-range interactions. In this work, single cis-(1R,2S)-2-aminocyclohexanecarboxylic acid mutations were introduced into the edge strands of the eight-stranded β-sandwich mimetic structures from the betabellin family. Temperature-dependent NMR and CD measurements, together with thermodynamic analyses, demonstrated that the modified peripheral strands exhibited an irregular and partially disordered structure but were able to exert sufficient shielding on the hydrophobic core to retain the predominantly β-sandwich structure. Although the frustrated interactions decreased the free energy of unfolding, the temperature of the maximum stabilities increased to or remained at physiologically relevant temperatures. We found that the irregular peripheral strands were able to prevent edge-to-edge association and fibril formation in the aggregation-prone model. These findings establish a β-sandwich stabilization and aggregation inhibition approach, which does not interfere with the pillars of the peptide bond or change the net charge of the peptide.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary.
| | - Titanilla Szögi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Tamás A Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
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19
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Cabalteja CC, Mihalko DS, Seth Horne W. Heterogeneous-Backbone Foldamer Mimics of a Computationally Designed, Disulfide-Rich Miniprotein. Chembiochem 2019; 20:103-110. [PMID: 30326175 PMCID: PMC6314896 DOI: 10.1002/cbic.201800558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/29/2022]
Abstract
Disulfide-rich peptides have found widespread use in the development of bioactive agents; however, low proteolytic stability and the difficulty of exerting synthetic control over chain topology present barriers to their application in some systems. Herein, we report a method that enables the creation of artificial backbone ("foldamer") mimics of compact, disulfide-rich tertiary folds. Systematic replacement of a subset of natural α-residues with various artificial building blocks in the context of a computationally designed prototype sequence leads to "heterogeneous-backbone" variants that undergo clean oxidative folding, adopt tertiary structures indistinguishable from that of the prototype, and enjoy proteolytic protection beyond that inherent to the topologically constrained scaffold. Collectively, these results demonstrate systematic backbone substitution to be a viable method to engineer the properties of disulfide-rich sequences and expands the repertoire of protein mimicry by foldamers to an exciting new structural class.
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Affiliation(s)
- Chino C. Cabalteja
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 (USA)
| | - Daniel S. Mihalko
- 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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20
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Fisher BF, Hong SH, Gellman SH. Thermodynamic Scale of β-Amino Acid Residue Propensities for an α-Helix-like Conformation. J Am Chem Soc 2018; 140:9396-9399. [PMID: 30022665 PMCID: PMC6095142 DOI: 10.1021/jacs.8b05162] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A thiol-thioester exchange system has been used to measure the propensities of diverse β-amino acid residues to participate in an α-helix-like conformation. These measurements depend on formation of a parallel coiled-coil tertiary structure when two peptide segments become linked by thioester formation. One peptide segment contains a "guest" site that accommodates diverse β residues and is distal to the coiled-coil interface. We find that helix propensity is influenced by side chain placement within the β residue [β3 (side chain adjacent to nitrogen) slightly favored relative to β2 (side chain adjacent to carbonyl)]. The previously recognized helix stabilization resulting from five-membered ring incorporation is quantified. These results are significant because so few quantitative thermodynamic measurements have been reported for α/β-peptide folding.
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Affiliation(s)
| | | | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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21
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Abstract
The prospect of recreating the complex structural hierarchy of protein folding in synthetic oligomers with backbones that are artificial in covalent structure ("foldamers") has long fascinated chemists. Foldamers offer complex functions from biostable scaffolds and have found widespread applications in fields from biomedical to materials science. Most precedent has focused on isolated secondary structures or their assemblies. In considering the goal of complex protein-like tertiary folding patterns, a key barrier became apparent. How does one design a backbone with covalent connectivity and a sequence of side-chain functional groups that will support defined intramolecular packing of multiple artificial secondary structures? Two developments were key to overcoming this challenge. First was the recognition of the power of blending α-amino acid residues with monomers differing in backbone connectivity to create "heterogeneous-backbone" foldamers. Second was the finding that replacing some of the natural α-residues in a biological sequence with artificial-backbone variants can result in a mimic that retains both the fold and function of the native sequence and, in some cases, gains advantageous characteristics. Taken together, these precedents lead to a view of a protein as chemical entity having two orthogonal sequences: a sequence of side-chain functional groups and a separate sequence of backbone units displaying those functional groups. In this Account, we describe our lab's work over the last ∼10 years to leverage the above concept of protein sequence duality in order to develop design principles for constructing heterogeneous-backbone foldamers that adopt complex protein-like tertiary folds. Fundamental to the approach is the utilization of a variety of artificial building blocks (e.g., d-α-residues, Cα-Me-α-residues, N-Me-α-residues, β-residues, γ-residues, δ-residues, polymer segments) in concert, replacing a fraction of α-residues in a given prototype sequence. We provide an overview of the state-of-the-art in terms of design principles for choosing substitutions based on consideration of local secondary structure and retention of key side-chain functional groups. We survey high-resolution structures of backbone-modified proteins to illustrate how diverse artificial moieties are accommodated in tertiary fold contexts. We detail efforts to elucidate how backbone alteration impacts folding thermodynamics and describe how such data informs the development of improved design rules. Collectively, a growing body of results by our lab and others spanning multiple protein systems suggests there is a great deal of plasticity with respect to the backbone chemical structures upon which sequence-encoded tertiary folds can manifest. Moreover, these efforts suggest sequence-guided backbone alteration as a broadly applicable strategy for generating foldamers with complex tertiary folding patterns. We conclude by offering some perspective regarding the near future of this field, in terms of unanswered questions, technological needs, and opportunities for new areas of inquiry.
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Affiliation(s)
- Kelly L. George
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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22
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Mortenson DE, Kreitler DF, Thomas NC, Guzei IA, Gellman SH, Forest KT. Evaluation of β-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure. Chembiochem 2018; 19:604-612. [PMID: 29272560 DOI: 10.1002/cbic.201700580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Indexed: 01/16/2023]
Abstract
β-Amino acids have a backbone that is expanded by one carbon atom relative to α-amino acids, and β residues have been investigated as subunits in protein-like molecules that adopt discrete and predictable conformations. Two classes of β residue have been widely explored in the context of generating α-helix-like conformations: β3 -amino acids, which are homologous to α-amino acids and bear a side chain on the backbone carbon adjacent to nitrogen, and residues constrained by a five-membered ring, such the one derived from trans-2-aminocyclopentanecarboxylic acid (ACPC). Substitution of α residues with their β3 homologues within an α-helix-forming sequence generally causes a decrease in conformational stability. Use of a ring-constrained β residue, however, can offset the destabilizing effect of α→β substitution. Here we extend the study of α→β substitutions, involving both β3 and ACPC residues, to short loops within a small tertiary motif. We start from previously reported variants of the Pin1 WW domain that contain a two-, three-, or four-residue β-hairpin loop, and we evaluate α→β replacements at each loop position for each variant. By referral to the ϕ,ψ angles of the native structure, one can choose a stereochemically appropriate ACPC residue. Use of such logically chosen ACPC residues enhances conformational stability in several cases. Crystal structures of three β-containing Pin1 WW domain variants show that a native-like tertiary structure is maintained in each case.
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Affiliation(s)
- David E Mortenson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Dale F Kreitler
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Nicole C Thomas
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Ilia A Guzei
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Katrina T Forest
- Departments of Chemistry and Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA
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23
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Haney CM, Werner HM, McKay JJ, Horne WS. Thermodynamic origin of α-helix stabilization by side-chain cross-links in a small protein. Org Biomol Chem 2018; 14:5768-73. [PMID: 27006192 DOI: 10.1039/c6ob00475j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Peptide cross-linking has been widely explored as a means of constraining short sequences into stable folded conformations, most commonly α-helices. The prevailing hypothesis for the origin of helix stabilization is an entropic effect resulting from backbone pre-organization; however, obtaining direct evidence bearing on this hypothesis is challenging. Here, we compare the folding thermodynamics of a small helix-rich protein domain and analogues containing one of three common cross-linking motifs. Analysis of the folding free energy landscapes of linear vs. cyclized species reveal consistent trends in the effect of cyclization on folding energetics, as well as subtle differences based on the chemistry of the cross link. Stabilization in all three systems arises entirely from a reduction in the entropic penalty of folding that more than compensates for an enthalpic destabilization of the folded state.
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Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - Halina M Werner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - James J McKay
- 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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24
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Lang K. Building Peptide Bonds in Haifa: The Seventh Chemical Protein Synthesis (CPS) Meeting. Chembiochem 2018; 19:115-120. [PMID: 29251813 DOI: 10.1002/cbic.201700606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 01/24/2023]
Abstract
The power of CPS, live! More than 90 attendees from around the world came together in Haifa to present and hear about cutting-edge science in protein chemistry, from advances in synthetic methods to applications in biology and medicine. The meeting was a powerful demonstration that chemical protein synthesis can provide otherwise unattainable insights into protein structure and function.
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Affiliation(s)
- Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstrasse 4, 85748, Garching, Germany
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25
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Zhao D, Yang L, Yuan Y, Wang H, Dong H, Li S. Molecular Mechanism of Self-Assembly of Aromatic Oligoamides into Interlocked Double-Helix Foldamers. J Phys Chem B 2017; 121:10064-10072. [PMID: 29019673 DOI: 10.1021/acs.jpcb.7b09067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Foldamer, inspired by the structures and functions of biopolymers, is defined as an artificial molecular architecture that can fold into a three-dimensional structure in solution and has been a growing and active field in supramolecular chemistry. The central issue in foldamer science is to understand how the primary sequence of oligomer folds into conformationally ordered structures as well as how individual subunits self-associate into assembly. For duplex structures, these two issues are always interrelated and inseparable with each other. Although the emergence of new foldamer keeps growing, the detailed mechanism remains elusive. On the basis of an artificially synthesized arylamide oligoamide foldamer with its crystal structure available, we constructed a set of four foldamers with a similar backbone but different substituents and aimed at dissecting the folding and self-association mechanisms of a double-helical foldamer with computations. Using molecular simulations at a microsecond time scale, we observed very consistent processes of the spontaneous self-assembly of two single-helical motifs into an entwined complex. Our results reveal that aggregation of two single-helical motifs driven by extensive π-π interactions is energetically favorable and that this spontaneous self-assembly proceeds through an "unwinding-threading-rewinding" mechanism. The detailed mechanisms about the folding and self-assembly in an aromatic oligoamide foldamer we present here disclose how the sequence is associated with a well-ordered three-dimensional structure at atomic level and therefore may have implications for designing new foldamers with versatile functions.
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Affiliation(s)
| | - Ling Yang
- CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
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26
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Fisher BF, Hong SH, Gellman SH. Helix Propensities of Amino Acid Residues via Thioester Exchange. J Am Chem Soc 2017; 139:13292-13295. [PMID: 28898059 PMCID: PMC5995559 DOI: 10.1021/jacs.7b07930] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We describe the use of thioester exchange equilibria to measure the propensities of amino acid residues to participate in helical secondary structure at room temperature in the absence of denaturants. Thermally or chemically induced unfolding has previously been employed to measure α-helix propensities among proteinogenic α-amino acid residues, and quantitative comparison with precedents indicates that the thioester exchange system is reliable for residues that lack side chain charge. This system allows the measurement of α-helix propensities for d-α-amino acid residues and propensities of residues with nonproteinogenic backbones, such as those derived from a β-amino acid, to participate in an α-helix-like secondary structure.
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Affiliation(s)
- Brian F. Fisher
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Seong Ho Hong
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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27
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George KL, Horne WS. Heterogeneous-Backbone Foldamer Mimics of Zinc Finger Tertiary Structure. J Am Chem Soc 2017; 139:7931-7938. [PMID: 28509549 DOI: 10.1021/jacs.7b03114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A variety of oligomeric backbones with compositions deviating from biomacromolecules can fold in defined ways. Termed "foldamers," these agents have diverse potential applications. A number of protein-inspired secondary structures (e.g., helices, sheets) have been produced from unnatural backbones, yet examples of tertiary folds combining several secondary structural elements in a single entity are rare. One promising strategy to address this challenge is the systematic backbone alteration of natural protein sequences, through which a subset of the native side chains is displayed on an unnatural building block to generate a heterogeneous backbone. A drawback to this approach is that substitution at more than one or two sites often comes at a significant energetic cost to fold stability. Here we report heterogeneous-backbone foldamers that mimic the zinc finger domain, a ubiquitous and biologically important metal-binding tertiary motif, and do so with a folded stability that is superior to the natural protein on which their design is based. A combination of UV-vis spectroscopy, isothermal titration calorimetry, and multidimensional NMR reveals that suitably designed oligomers with >20% modified backbones can form native-like tertiary folds with metal-binding environments identical to the prototype sequence (the third finger of specificity factor 1) and enhanced thermodynamic stability. These results expand the scope of heterogeneous-backbone foldamer design to a new tertiary structure class and show that judiciously applied backbone modification can be accompanied by improvement to fold stability.
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Affiliation(s)
- Kelly L George
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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28
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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29
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Wang YJ, Szantai-Kis DM, Petersson EJ. Chemoselective modifications for the traceless ligation of thioamide-containing peptides and proteins. Org Biomol Chem 2016; 14:6262-9. [PMID: 27264841 DOI: 10.1039/c6ob01020b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Thioamides are single-atom substitutions of canonical amide bonds, and have been proven to be versatile and minimally perturbing probes in protein folding studies. Previously, our group showed that thioamides can be incorporated into proteins by native chemical ligation (NCL) with Cys as a ligation handle. In this study, we report the expansion of this strategy into non-Cys ligation sites, utilizing radical initiated desulfurization to "erase" the side chain thiol after ligation. The reaction exhibited high chemoselectivity against thioamides, which can be further enhanced with thioacetamide as a sacrificial scavenger. As a proof-of-concept example, we demonstrated the incorporation of a thioamide probe into a 56 amino acid protein, the B1 domain of Protein G (GB1). Finally, we showed that the method can be extended to β-thiol amino acid analogs and selenocysteine.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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30
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Kreitler DF, Mortenson DE, Forest KT, Gellman SH. Effects of Single α-to-β Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization. J Am Chem Soc 2016; 138:6498-505. [PMID: 27171550 DOI: 10.1021/jacs.6b01454] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic peptides that contain backbone modifications but nevertheless adopt folded structures similar to those of natural polypeptides are of fundamental interest and may provide a basis for biomedical applications. Such molecules can, for example, mimic the ability of natural prototypes to bind to specific target macromolecules but resist degradation by proteases. We have previously shown that oligomers containing mixtures of α- and β-amino acid residues ("α/β-peptides") can mimic the α-helix secondary structure, and that properly designed α/β-peptides can bind to proteins that evolved to bind to α-helical partners. Here we report fundamental studies that support the long-range goal of extending the α/β approach to tertiary structures. We have evaluated the impact of single α → β modifications on the structure and stability of the small and well-studied villin headpiece subdomain (VHP). The native state of this 35-residue polypeptide contains several α-helical segments packed around a small hydrophobic core. We examined α → β substitution at four solvent-exposed positions, Asn19, Trp23, Gln26 and Lys30. In each case, both the β(3) homologue of the natural α residue and a cyclic β residue were evaluated. All α → β(3) substitutions caused significant destabilization of the tertiary structure as measured by variable-temperature circular dichroism, although at some of these positions, replacing the β(3) residue with a cyclic β residue led to improved stability. Atomic-resolution structures of four VHP analogues were obtained via quasiracemic crystallization. These findings contribute to a fundamental α/β-peptide knowledge-base by confirming that β(3)-amino acid residues can serve as effective structural mimics of homologous α-amino acid residues within a natural tertiary fold, which should support rational design of functional α/β analogues of natural poly-α-peptides.
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Affiliation(s)
- Dale F Kreitler
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - David E Mortenson
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Katrina T Forest
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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31
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Tavenor NA, Reinert ZE, Lengyel GA, Griffith BD, Horne WS. Comparison of design strategies for α-helix backbone modification in a protein tertiary fold. Chem Commun (Camb) 2016; 52:3789-92. [PMID: 26853882 PMCID: PMC4767680 DOI: 10.1039/c6cc00273k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report here the comparison of five classes of unnatural amino acid building blocks for their ability to be accommodated into an α-helix in a protein tertiary fold context. High-resolution structural characterization and analysis of folding thermodynamics yield new insights into the relationship between backbone composition and folding energetics in α-helix mimetics and suggest refined design rules for engineering the backbones of natural sequences.
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Affiliation(s)
- Nathan A Tavenor
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - George A Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Brian D Griffith
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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32
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Werner HM, Cabalteja CC, Horne WS. Peptide Backbone Composition and Protease Susceptibility: Impact of Modification Type, Position, and Tandem Substitution. Chembiochem 2015. [PMID: 26205791 DOI: 10.1002/cbic.201500312] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The clinical utility of peptides is limited by their rapid degradation by endogenous proteases. Modification of the peptide backbone can generate functional analogues with enhanced proteolytic stability. Existing principles for the design of such oligomers have focused primarily on effective structural mimicry. A more robust strategy would incorporate a rational approach for engineering maximal proteolytic stability with minimal unnatural residue content. We report here the systematic comparison of the proteolytic resistance imparted by four backbone modifications commonly employed in the design of protease-stable analogues of peptides with complex folding patterns. The degree of protection was quantified as a function of modification type, position, and tandem substitution in the context of a long, unstructured host sequence and a canonical serine protease. These results promise to inform ongoing work to develop biostable mimics of increasingly complex peptides and proteins.
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Affiliation(s)
- Halina M Werner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA
| | - Chino C Cabalteja
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA.
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33
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Peterson-Kaufman KJ, Haase HS, Boersma MD, Lee EF, Fairlie WD, Gellman SH. Residue-Based Preorganization of BH3-Derived α/β-Peptides: Modulating Affinity, Selectivity and Proteolytic Susceptibility in α-Helix Mimics. ACS Chem Biol 2015; 10:1667-75. [PMID: 25946900 DOI: 10.1021/acschembio.5b00109] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report progress toward a general strategy for mimicking the recognition properties of specific α-helices within natural proteins through the use of oligomers that are less susceptible than conventional peptides to proteolysis. The oligomers contain both α- and β-amino acid residues, with the density of the β subunits low enough that an α-helix-like conformation can be adopted but high enough to interfere with protease activity. Previous studies with a different protein-recognition system that suggested ring-constrained β residues can be superior to flexible β residues in terms of maximizing α/β-peptide affinity for a targeted protein surface. Here, we use mimicry of the 18-residue Bim BH3 domain to expand the scope of this strategy. Two significant advances have been achieved. First, we have developed and validated a new ring-constrained β residue that bears an acidic side chain, which complements previously known analogues that are either hydrophobic or basic. Second, we have discovered that placing cyclic β residues at sites that make direct contact with partner proteins can lead to substantial discrimination between structurally homologous binding partners, the proteins Bcl-xL and Mcl-1. Overall, this study helps to establish that α/β-peptides containing ring-preorganized β residues can reliably provide proteolytically resistant ligands for proteins that naturally evolved to recognize α-helical partners.
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Affiliation(s)
| | - Holly S. Haase
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Melissa D. Boersma
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Erinna F. Lee
- Structural
Biology Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - W. Douglas Fairlie
- Structural
Biology Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
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34
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Werner HM, Horne WS. Folding and function in α/β-peptides: targets and therapeutic applications. Curr Opin Chem Biol 2015; 28:75-82. [PMID: 26136051 DOI: 10.1016/j.cbpa.2015.06.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/02/2015] [Accepted: 06/09/2015] [Indexed: 12/20/2022]
Abstract
Combining natural α-amino acid residues and unnatural β-amino acid residues in a single chain leads to heterogeneous-backbone oligomers called α/β-peptides. Despite their unnatural backbones, α/β-peptides can manifest a variety of folding patterns and biological functions reminiscent of natural peptides and proteins. Moreover, incorporation of β-residues can impart useful properties to the oligomer such as improved stability to degradation by protease enzymes. α/β-Peptides have been developed that engage diverse biological targets, including proteins involved in apoptotic signalling, HIV-cell fusion, hormone signalling, and angiogenesis. For some systems, promising results obtained in vitro have paved the way for demonstrated activity in vivo, where α/β-peptides show equal potency and improved duration of effect compared to α-peptide counterparts.
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Affiliation(s)
- Halina M Werner
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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35
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Reinert ZE, Horne WS. Protein backbone engineering as a strategy to advance foldamers toward the frontier of protein-like tertiary structure. Org Biomol Chem 2014; 12:8796-802. [PMID: 25285575 PMCID: PMC4211622 DOI: 10.1039/c4ob01769b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A variety of non-biological structural motifs have been incorporated into the backbone of natural protein sequences. In parallel work, diverse unnatural oligomers of de novo design (termed "foldamers") have been developed that fold in defined ways. In this Perspective article, we survey foundational studies on protein backbone engineering, with a focus on alterations made in the context of complex tertiary folds. We go on to summarize recent work illustrating the potential promise of these methods to provide a general framework for the construction of foldamer mimics of protein tertiary structures.
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Affiliation(s)
- Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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