1
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Cao L, Coventry B, Goreshnik I, Huang B, Sheffler W, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D. Design of protein-binding proteins from the target structure alone. Nature 2022; 605:551-560. [PMID: 35332283 PMCID: PMC9117152 DOI: 10.1038/s41586-022-04654-9] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/15/2022] [Indexed: 12/03/2022]
Abstract
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1-5. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
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Affiliation(s)
- Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Buwei Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joon Sung Park
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Iva Marković
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Rameshwar U Kadam
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Koen H G Verschueren
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kenneth Verstraete
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Scott Thomas Russell Walsh
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- J.A.M.E.S. Farm, Clarksville, MD, USA
| | - Nathaniel Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Ashish Phal
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Aerin Yang
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michelle DeWitt
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lora Picton
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren Miller
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Eva-Maria Strauch
- Deptartment of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Nicholas D DeBouver
- UCB Pharma, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Allison Pires
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
- Seattle Children's Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Samer Halabiya
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Bradley Hammerson
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Steffen Bernard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Sangwon Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Savvas N Savvides
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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3
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Doolan AM, Rennie ML, Crowley PB. Protein Recognition by Functionalized Sulfonatocalix[4]arenes. Chemistry 2017; 24:984-991. [PMID: 29125201 DOI: 10.1002/chem.201704931] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/31/2022]
Abstract
The interactions of two mono-functionalized sulfonatocalix[4]arenes with cytochrome c were investigated by structural and thermodynamic methods. The replacement of a single sulfonate with either a bromo or a phenyl substituent resulted in altered recognition of cytochrome c as evidenced by X-ray crystallography. The bromo-substituted ligand yielded a new binding mode in which a self-encapsulated calixarene dimer contributed to crystal packing. This ligand also formed a weak halogen bond with the protein. The phenyl-substituted ligand was bound to Lys4 of cytochrome c, in a 1.7 Å resolution crystal structure. A dimeric packing arrangement mediated by ligand-ligand contacts in the crystal suggested a possible assembly mechanism. The different protein recognition properties of these calixarenes are discussed.
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Affiliation(s)
- Aishling M Doolan
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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4
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5
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Da Fonseca I, Qureshi IA, Mehra-Chaudhary R, Kizjakina K, Tanner JJ, Sobrado P. Contributions of unique active site residues of eukaryotic UDP-galactopyranose mutases to substrate recognition and active site dynamics. Biochemistry 2014; 53:7794-804. [PMID: 25412209 PMCID: PMC4270374 DOI: 10.1021/bi501008z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
UDP-galactopyranose mutase (UGM)
catalyzes the interconversion
between UDP-galactopyranose and UDP-galactofuranose. Absent in humans,
galactofuranose is found in bacterial and fungal cell walls and is
a cell surface virulence factor in protozoan parasites. For these
reasons, UGMs are targets for drug discovery. Here, we report a mutagenesis
and structural study of the UGMs from Aspergillus fumigatus and Trypanosoma cruzi focused on
active site residues that are conserved in eukaryotic UGMs but are
absent or different in bacterial UGMs. Kinetic analysis of the variants
F66A, Y104A, Q107A, N207A, and Y317A (A. fumigatus numbering) show decreases in kcat/KM values of 200–1000-fold for the mutase
reaction. In contrast, none of the mutations significantly affect
the kinetics of enzyme activation by NADPH. These results indicate
that the targeted residues are important for promoting the transition
state conformation for UDP-galactofuranose formation. Crystal structures
of the A. fumigatus mutant enzymes
were determined in the presence and absence of UDP to understand the
structural consequences of the mutations. The structures suggest important
roles for Asn207 in stabilizing the closed active site, and Tyr317
in positioning of the uridine ring. Phe66 and the corresponding residue
in Mycobacterium tuberculosis UGM (His68)
play a role as the backstop, stabilizing the galactopyranose group
for nucleophilic attack. Together, these results provide insight into
the essentiality of the targeted residues for realizing maximal catalytic
activity and a proposal for how conformational changes that close
the active site are temporally related and coupled together.
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Affiliation(s)
- Isabel Da Fonseca
- Department of Biochemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
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6
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Culpepper MA, Rosenzweig AC. Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 2014; 53:6211-9. [PMID: 25185034 PMCID: PMC4188263 DOI: 10.1021/bi500850j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
In
the initial steps of their metabolic pathway, methanotrophic
bacteria oxidize methane to methanol with methane monooxygenases (MMOs)
and methanol to formaldehyde with methanol dehydrogenases (MDHs).
Several lines of evidence suggest that the membrane-bound or particulate
MMO (pMMO) and MDH interact to form a metabolic supercomplex. To further
investigate the possible existence of such a supercomplex, native
MDH from Methylococcus capsulatus (Bath) has been
purified and characterized by size exclusion chromatography with multi-angle
light scattering and X-ray crystallography. M. capsulatus (Bath) MDH is primarily a dimer in solution, although an oligomeric
species with a molecular mass of ∼450–560 kDa forms
at higher protein concentrations. The 2.57 Å resolution crystal
structure reveals an overall fold and α2β2 dimeric architecture similar to those of other MDH structures.
In addition, biolayer interferometry studies demonstrate specific
protein–protein interactions between MDH and M. capsulatus (Bath) pMMO as well as between MDH and the truncated recombinant
periplasmic domains of M. capsulatus (Bath) pMMO
(spmoB). These interactions exhibit KD values of 833 ± 409 nM and 9.0 ± 7.7 μM, respectively.
The biochemical data combined with analysis of the crystal lattice
interactions observed in the MDH structure suggest a model in which
MDH and pMMO associate not as a discrete, stoichiometric complex but
as a larger assembly scaffolded by the intracytoplasmic membranes.
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Affiliation(s)
- Megen A Culpepper
- Departments of Molecular Biosciences and Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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7
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Kumar R, Matsumura H, Lovell S, Yao H, Rodríguez JC, Battaile KP, Moënne-Loccoz P, Rivera M. Replacing the axial ligand tyrosine 75 or its hydrogen bond partner histidine 83 minimally affects hemin acquisition by the hemophore HasAp from Pseudomonas aeruginosa. Biochemistry 2014; 53:2112-25. [PMID: 24625274 PMCID: PMC3985777 DOI: 10.1021/bi500030p] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hemophores from Pseudomonas aeruginosa (HasAp), Serratia marcescens (HasAsm), and Yersinia pestis (HasAyp) bind hemin between two loops. One of the loops harbors conserved axial ligand Tyr75 (Y75 loop) in all three structures, whereas the second loop (H32 loop) contains axial ligand His32 in HasAp and HasAsm, but a noncoordinating Gln32 in HasAyp. Binding of hemin to the Y75 loop of HasAp or HasAsm causes a large rearrangement of the H32 loop that allows His32 coordination. The Q32 loop in apo-HasAyp is already in the closed conformation, such that binding of hemin to the conserved Y75 loop occurs with minimal structural rearrangement and without coordinative interaction with the Q32 loop. In this study, structural and spectroscopic investigations of the hemophore HasAp were conducted to probe (i) the role of the conserved Tyr75 loop in hemin binding and (ii) the proposed requirement of the His83-Tyr75 hydrogen bond to allow the coordination of hemin by Tyr75. High-resolution crystal structures of H83A holo-HasAp obtained at pH 6.5 (0.89 Å) and pH 5.4 (1.25 Å) show that Tyr75 remains coordinated to the heme iron, and that a water molecule can substitute for Nδ of His83 to interact with the Oη atom of Tyr75, likely stabilizing the Tyr75-Fe interaction. Nuclear magnetic resonance spectroscopy revealed that in apo-Y75A and apo-H83A HasAp, the Y75 loop is disordered, and that disorder propagates to nearby elements of secondary structure, suggesting that His83 Nδ-Tyr75 Oη interaction is important to the organization of the Y75 loop in apo-HasA. Kinetic analysis of hemin loading conducted via stopped-flow UV-vis and rapid-freeze-quench resonance Raman shows that both mutants load hemin with biphasic kinetic parameters that are not significantly dissimilar from those previously observed for wild-type HasAp. When the structural and kinetic data are taken together, a tentative model emerges, which suggests that HasA hemophores utilize hydrophobic, π-π stacking, and van der Waals interactions to load hemin efficiently, while axial ligation likely functions to slow hemin release, thus allowing the hemophore to meet the challenge of capturing hemin under inhospitable conditions and delivering it selectively to its cognate receptor.
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Affiliation(s)
- Ritesh Kumar
- Department of Chemistry, University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive, Lawrence, Kansas 66047, United States
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8
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Certal V, Carry JC, Halley F, Virone-Oddos A, Thompson F, Filoche-Rommé B, El-Ahmad Y, Karlsson A, Charrier V, Delorme C, Rak A, Abecassis PY, Amara C, Vincent L, Bonnevaux H, Nicolas JP, Mathieu M, Bertrand T, Marquette JP, Michot N, Benard T, Perrin MA, Lemaitre O, Guerif S, Perron S, Monget S, Gruss-Leleu F, Doerflinger G, Guizani H, Brollo M, Delbarre L, Bertin L, Richepin P, Loyau V, Garcia-Echeverria C, Lengauer C, Schio L. Discovery and Optimization of Pyrimidone Indoline Amide PI3Kβ Inhibitors for the Treatment of Phosphatase and Tensin Homologue (PTEN)-Deficient Cancers. J Med Chem 2014; 57:903-20. [DOI: 10.1021/jm401642q] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victor Certal
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Jean-Christophe Carry
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Frank Halley
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Angela Virone-Oddos
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Fabienne Thompson
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Bruno Filoche-Rommé
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Youssef El-Ahmad
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Andreas Karlsson
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Véronique Charrier
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Cécile Delorme
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Alexey Rak
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Pierre-Yves Abecassis
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Céline Amara
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Loïc Vincent
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Hélène Bonnevaux
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Jean-Paul Nicolas
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Magali Mathieu
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Thomas Bertrand
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Jean-Pierre Marquette
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Nadine Michot
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Tsiala Benard
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Marc-Antoine Perrin
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Olivier Lemaitre
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Stephane Guerif
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Sébastien Perron
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Sylvie Monget
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Florence Gruss-Leleu
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Gilles Doerflinger
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Houlfa Guizani
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Maurice Brollo
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Laurence Delbarre
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Luc Bertin
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Patrick Richepin
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Véronique Loyau
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Carlos Garcia-Echeverria
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Christoph Lengauer
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Laurent Schio
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
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9
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Chadegani F, Lovell S, Mullangi V, Miyagi M, Battaile KP, Bann JG. (19)F nuclear magnetic resonance and crystallographic studies of 5-fluorotryptophan-labeled anthrax protective antigen and effects of the receptor on stability. Biochemistry 2014; 53:690-701. [PMID: 24387629 PMCID: PMC3985773 DOI: 10.1021/bi401405s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The anthrax protective antigen (PA)
is an 83 kDa protein that is
one of three protein components of the anthrax toxin, an AB toxin
secreted by Bacillus anthracis. PA is capable of
undergoing several structural changes, including oligomerization to
either a heptameric or octameric structure called the prepore, and
at acidic pH a major conformational change to form a membrane-spanning
pore. To follow these structural changes at a residue-specific level,
we have conducted initial studies in which we have biosynthetically
incorporated 5-fluorotryptophan (5-FTrp) into PA, and we have studied
the influence of 5-FTrp labeling on the structural stability of PA
and on binding to the host receptor capillary morphogenesis protein
2 (CMG2) using 19F nuclear magnetic resonance (NMR). There
are seven tryptophans in PA, but of the four domains in PA, only two
contain tryptophans: domain 1 (Trp65, -90, -136, -206, and -226) and
domain 2 (Trp346 and -477). Trp346 is of particular interest because
of its proximity to the CMG2 binding interface, and because it forms
part of the membrane-spanning pore. We show that the 19F resonance of Trp346 is sensitive to changes in pH, consistent with
crystallographic studies, and that receptor binding significantly
stabilizes Trp346 to both pH and temperature. In addition, we provide
evidence that suggests that resonances from tryptophans distant from
the binding interface are also stabilized by the receptor. Our studies
highlight the positive impact of receptor binding on protein stability
and the use of 19F NMR in gaining insight into structural
changes in a high-molecular weight protein.
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Affiliation(s)
- Fatemeh Chadegani
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
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10
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Liu Y, Olanrewaju YO, Zhang X, Cheng X. DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at an atomic resolution of 0.97 Å. Biochemistry 2013; 52:9310-7. [PMID: 24236546 DOI: 10.1021/bi401360n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Zfp57 gene encodes a KRAB (Krüppel-associated box) domain-containing C2H2 zinc finger transcription factor that is expressed in early development. Zfp57 protein recognizes methylated CpG dinucleotide within GCGGCA elements at multiple imprinting control regions. In the previously determined structure of the mouse Zfp57 DNA-binding domain in complex with DNA containing 5-methylcytosine (5mC), the side chains of Arg178 and Glu182 contact the methyl group via hydrophobic and van der Waals interactions. We examined the role of Glu182 in recognition of 5mC by mutagenesis. The majority of mutants examined lose selectivity of methylated (5mC) over unmodified (C) and oxidative derivatives, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC), suggesting that the side chain of Glu182 (the size and the charge) is dispensable for methyl group recognition but negatively impacts the binding of unmodified cytosine as well as oxidized derivatives of 5mC to achieve 5mC selectivity. Substitution of Glu182 with its corresponding amide (E182Q) had no effect on methylated DNA binding but gained significant binding affinity for 5caC DNA, resulting in a binding affinity for 5caC DNA comparable to that of the wild-type protein for 5mC. We show structurally that the uncharged amide group of E182Q interacts favorably with the carboxylate group of 5caC. Furthermore, introducing a positively charged arginine at position 182 resulted in a mutant (E182R) having higher selectivity for the negatively charged 5caC.
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Affiliation(s)
- Yiwei Liu
- Department of Biochemistry, Emory University School of Medicine , 1510 Clifton Road, Atlanta, Georgia 30322, United States
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11
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Elkins JM, Wang J, Deng X, Pattison MJ, Arthur JSC, Erazo T, Gomez N, Lizcano JM, Gray NS, Knapp S. X-ray crystal structure of ERK5 (MAPK7) in complex with a specific inhibitor. J Med Chem 2013; 56:4413-21. [PMID: 23656407 PMCID: PMC3683888 DOI: 10.1021/jm4000837] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The
protein kinase ERK5 (MAPK7) is an emerging drug target for
a variety of indications, in particular for cancer where it plays
a key role mediating cell proliferation, survival, epithelial–mesenchymal
transition, and angiogenesis. To date, no three-dimensional structure
has been published that would allow rational design of inhibitors.
To address this, we determined the X-ray crystal structure of the
human ERK5 kinase domain in complex with a highly specific benzo[e]pyrimido[5,4-b]diazepine-6(11H)-one inhibitor. The structure reveals that specific residue
differences in the ATP-binding site, compared to the related ERKs
p38s and JNKs, allow for the development of ERK5-specific inhibitors.
The selectivity of previously observed ERK5 inhibitors can also be
rationalized using this structure, which provides a template for future
development of inhibitors with potential for treatment of disease.
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Affiliation(s)
- Jonathan M Elkins
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
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12
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Pryor JM, Gakhar L, Washington MT. Structure and functional analysis of the BRCT domain of translesion synthesis DNA polymerase Rev1. Biochemistry 2013; 52:254-63. [PMID: 23240687 PMCID: PMC3580236 DOI: 10.1021/bi301572z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Translesion synthesis (TLS) is a pathway in which specialized, low-fidelity DNA polymerases are used to overcome replication blocks caused by DNA damage. The use of this pathway often results in somatic mutations that can drive carcinogenesis. Rev1 is a TLS polymerase found in all eukaryotes that plays a pivotal role in mediating DNA damage-induced mutagenesis. It possesses a BRCA1 C-terminal (BRCT) domain that is required for its function. The rev1-1 allele encodes a mutant form of Rev1 with a G193R substitution in this domain, which reduces the level of DNA damage-induced mutagenesis. Despite its clear importance in mutagenic TLS, the role of the BRCT domain is unknown. Here, we report the X-ray crystal structure of the yeast Rev1 BRCT domain and show that substitutions in residues constituting its phosphate-binding pocket do not affect mutagenic TLS. This suggests that the role of the Rev1 BRCT domain is not to recognize phosphate groups on protein binding partners or on DNA. We also found that residue G193 is located in a conserved turn region of the BRCT domain, and our in vivo and in vitro studies suggest that the G193R substitution may disrupt Rev1 function by destabilizing the fold of the BRCT domain.
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Affiliation(s)
- John M. Pryor
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Lokesh Gakhar
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Protein Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - M. Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
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13
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Yao H, Wang Y, Lovell S, Kumar R, Ruvinsky AM, Battaile KP, Vakser IA, Rivera M. The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin. J Am Chem Soc 2012; 134:13470-81. [PMID: 22812654 PMCID: PMC3428730 DOI: 10.1021/ja305180n] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ferritin-like molecules are unique to cellular iron homeostasis because they can store iron at concentrations much higher than those dictated by the solubility of Fe(3+). Very little is known about the protein interactions that deliver iron for storage or promote the mobilization of stored iron from ferritin-like molecules. Here, we report the X-ray crystal structure of Pseudomonas aeruginosa bacterioferritin (Pa-BfrB) in complex with bacterioferritin-associated ferredoxin (Pa-Bfd) at 2.0 Å resolution. As the first example of a ferritin-like molecule in complex with a cognate partner, the structure provides unprecedented insight into the complementary interface that enables the [2Fe-2S] cluster of Pa-Bfd to promote heme-mediated electron transfer through the BfrB protein dielectric (~18 Å), a process that is necessary to reduce the core ferric mineral and facilitate mobilization of Fe(2+). The Pa-BfrB-Bfd complex also revealed the first structure of a Bfd, thus providing a first view to what appears to be a versatile metal binding domain ubiquitous to the large Fer2_BFD family of proteins and enzymes with diverse functions. Residues at the Pa-BfrB-Bfd interface are highly conserved in Bfr and Bfd sequences from a number of pathogenic bacteria, suggesting that the specific recognition between Pa-BfrB and Pa-Bfd is of widespread significance to the understanding of bacterial iron homeostasis.
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Affiliation(s)
- Huili Yao
- Department of Chemistry, University of Kansas, Multidisciplinary Research Building, 2030 Becker Dr., Lawrence, KS 66047
| | - Yan Wang
- Department of Chemistry, University of Kansas, Multidisciplinary Research Building, 2030 Becker Dr., Lawrence, KS 66047
| | - Scott Lovell
- Del Shankel Structural Biology Center, University of Kansas, 2034 Becker Dr., Lawrence, KS 66047
| | - Ritesh Kumar
- Center for Bioinformatics, University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Anatoly M. Ruvinsky
- Center for Bioinformatics, University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman Woodward Medical Research Institute, 9700 S. Cass Avenue, Bldg. 435A, Argonne, IL 60439
| | - Ilya A. Vakser
- Center for Bioinformatics, University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Mario Rivera
- Department of Chemistry, University of Kansas, Multidisciplinary Research Building, 2030 Becker Dr., Lawrence, KS 66047
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14
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Affiliation(s)
- Phil Evans
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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