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Zhao G, Richaud AD, Williamson RT, Feig M, Roche SP. De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS Chem Biol 2024; 19:1583-1592. [PMID: 38916527 DOI: 10.1021/acschembio.4c00236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and noncanonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone β-hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue, highly conserved across CDR-H3 sequences, was found to extend the kinked base of these β-bulges through a combination of stabilizing intramolecular hydrogen bond and CH/π interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that β-bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics.
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Affiliation(s)
- Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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2
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Imani Z, Mundlapati VR, Brenner V, Gloaguen E, Le Barbu-Debus K, Zehnacker-Rentien A, Robin S, Aitken DJ, Mons M. Non-covalent interactions reveal the protein chain δ conformation in a flexible single-residue model. Chem Commun (Camb) 2023; 59:1161-1164. [PMID: 36625351 DOI: 10.1039/d2cc06658k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The δ conformation is a local secondary structure in proteins that implicates a πamide N-H⋯N interaction between a backbone N atom and the NH of the following residue. Small-molecule models thereof have been limited so far to rigid proline-type compounds. We show here that in derivatives of a cyclic amino acid with a sulphur atom in the γ-position, specific side-chain/backbone N-H⋯S interactions stabilize the δ conformation sufficiently to allow it to compete with classical C5 and C7 H-bonded conformers.
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Affiliation(s)
- Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France
| | | | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette 91191, France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette 91191, France
| | | | | | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.,Université de Paris, Faculté de Pharmacie, Paris 75006, France
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette 91191, France
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3
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O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding. Proteins 2022; 90:1159-1169. [DOI: 10.1002/prot.26298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/07/2022]
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4
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Baruah K, Sahariah B, Sakpal SS, Deka JKR, Bar AK, Bagchi S, Sarma BK. Stabilization of Azapeptides by N amide···H-N amide Hydrogen Bonds. Org Lett 2021; 23:4949-4954. [PMID: 34060858 DOI: 10.1021/acs.orglett.1c01111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An unusual Namide···H-Namide hydrogen bond (HB) was previously proposed to stabilize the azapeptide β-turns. Herein we provide experimental evidence for the Namide···H-Namide HB and show that this HB endows a stabilization of 1-3 kcal·mol-1 and enforces the trans-cis-trans (t-c-t) and cis-cis-trans (c-c-t) amide bond conformations in azapeptides and N-methyl-azapeptides, respectively. Our results indicate that these Namide···H-Namide HBs can have stabilizing contributions even in short azapeptides that cannot fold to form β-turns.
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Affiliation(s)
- Kalpita Baruah
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, Karnataka 560064, India
| | - Sushil S Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Jugal Kishore Rai Deka
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Arun Kumar Bar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 501507, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, Karnataka 560064, India
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5
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Dhar J, Kishore R, Chakrabarti P. Delineation of a new structural motif involving NHN γ-turn. Proteins 2019; 88:431-439. [PMID: 31587358 DOI: 10.1002/prot.25820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non-redundant protein chains reveals the existence of a three-residue, (i - 1) to (i + 1), structural motif, having two hydrogen-bonded five-membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side-chain at (i-1) and the main-chain NH of (i + 1). The average backbone torsion angles of -76(±21)° and - 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ-turn. Indeed, a search of three-residue fragments with restriction on the terminal Cα ···Cα distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ-turn, distinct from the NHO γ-turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main-chain atoms. As in the latter, the newly identified γ-turns are also of two types-classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.
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Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, Kolkata, India
| | - Raghuvansh Kishore
- Department of Zoology and Department of Biotechnology, Mizoram University, Aizawl, India
| | - Pinak Chakrabarti
- Bioinformatics Centre, Bose Institute, Kolkata, India.,Department of Biochemistry, Bose Institute, Kolkata, India
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6
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Dhar J, Chakrabarti P. Structural motif, topi and its role in protein function and fibrillation. Mol Omics 2018; 14:247-256. [PMID: 29896602 DOI: 10.1039/c8mo00048d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A protein chain is arranged into regions in which the backbone is organized into regular patterns (of conformation and hydrogen bonding) to form the most common secondary structures, α-helix and β-sheet, which are interspersed by turns and more irregular loop regions. A structural motif, topi, is discussed in which a pair of 2-residue segments, each containing hydrogen-bonded five-membered fused-ring motifs, distant in sequence are linked to each other by a hydrogen bond. Though a small motif, it appears to be important in the context of local folding patterns of proteins and occurs near protein active sites. The motif shows quite significant residue preference, and a Cys (or Ser) occupying the second position may further stabilize the motif by forming an additional hydrogen bond across it. Remarkably, topi is found within disease causing misfolded proteins, such as the fibrilled form of Aβ42, and also across the interface between two protein chains. This motif may be an important component of fibrillation and useful for modeling loop regions.
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Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
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Holcomb M, Adhikary R, Zimmermann J, Romesberg FE. Topological Evidence of Previously Overlooked Ni+1–H···Ni H-Bonds and Their Contribution to Protein Structure and Stability. J Phys Chem A 2017; 122:446-450. [DOI: 10.1021/acs.jpca.7b11013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Ramek M, Marković M, Loher C, Sabolović J. Pronounced conformational flexibility of physiological ( l -histidinato)( l -threoninato)copper(II) in aqueous solution disclosed by a quantum chemical study. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.06.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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