1
|
Ravikumar A, de Brevern AG, Srinivasan N. Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility. J Phys Chem B 2021; 125:2597-2606. [PMID: 33666418 DOI: 10.1021/acs.jpcb.1c00168] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Studies on energy associated with free dipeptides have shown that conformers with unfavorable (ϕ,ψ) torsion angles have higher energy compared to conformers with favorable (ϕ,ψ) angles. It is expected that higher energy confers higher dynamics and flexibility to that part of the protein. Here, we explore a potential relationship between conformational strain in a residue due to unfavorable (ϕ,ψ) angles and its flexibility and dynamics in the context of protein structures. We compared flexibility of strained and relaxed residues, which are recognized based on outlier/allowed and favorable (ϕ,ψ) angles respectively, using normal-mode analysis (NMA). We also performed in-depth analysis on flexibility and dynamics at catalytic residues in protein kinases, which exhibit different strain status in different kinase structures using NMA and molecular dynamics simulations. We underline that strain of a residue, as defined by backbone torsion angles, is almost unrelated to the flexibility and dynamics associated with it. Even the overall trend observed among all high-resolution structures in which relaxed residues tend to have slightly higher flexibility than strained residues is counterintuitive. Consequently, we propose that identifying strained residues based on (ϕ,ψ) values is not an effective way to recognize energetic strain in protein structures.
Collapse
Affiliation(s)
- Ashraya Ravikumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India, 560012
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, Paris F-75739, France.,University of Paris, Paris F-75739, France.,Institut National de la Transfusion Sanguine (INTS), Paris F-75739, France.,Laboratoire d'Excellence GR-Ex, Paris F-75739, France
| | | |
Collapse
|
2
|
Structural Basis and Binding Kinetics of Vaborbactam in Class A β-Lactamase Inhibition. Antimicrob Agents Chemother 2020; 64:AAC.00398-20. [PMID: 32778546 DOI: 10.1128/aac.00398-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022] Open
Abstract
Class A β-lactamases are a major cause of β-lactam resistance in Gram-negative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A β-lactamases, including CTX-M extended-spectrum β-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-Å crystal structure of CTX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-Å crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the β3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved β-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
Collapse
|
3
|
Majewski M, Ruiz-Carmona S, Barril X. An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Commun Chem 2019. [DOI: 10.1038/s42004-019-0205-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
The predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. However, structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, it entails an entropic penalty that counters complex formation. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Since hydrogen bonds have been described as essential for structural stability, here we investigate 469 such interactions across two diverse structure sets, comprising of 79 drug-like and 27 fragment ligands, respectively. Completely constricted protein-ligand complexes are rare and may fulfill a functional role. Most complexes balance order and disorder by combining a single anchoring point with looser regions. 25% do not contain any robust hydrogen bond and may form loose structures. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.
Collapse
|
4
|
Johnson TW, Gallego RA, Brooun A, Gehlhaar D, McTigue M. Reviving B-Factors: Retrospective Normalized B-Factor Analysis of c-ros Oncogene 1 Receptor Tyrosine Kinase and Anaplastic Lymphoma Kinase L1196M with Crizotinib and Lorlatinib. ACS Med Chem Lett 2018; 9:878-883. [PMID: 30258534 DOI: 10.1021/acsmedchemlett.8b00147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/18/2018] [Indexed: 11/28/2022] Open
Abstract
Structure-based drug design (SBDD) is commonly leveraged in rational drug design. Usually, ligand and binding site atomic coordinates from crystallographic data are exploited to optimize potency and selectivity. In addition to traditional, static views of proteins and ligands, we propose using normalized B-factors to study protein dynamics as a part of the drug optimization process. A retrospective case study of crizotinib and lorlatinib bound to both c-ros oncogene 1 kinase (ROS1) and anaplastic lymphoma kinase (ALK) L1196M related normalized B-factors to differences in binding affinity. This analysis showed that ligand binding can have protein-stabilizing effects that start near the ligand but propagate through nearby residues and structural waters to more distal motifs. The potential opportunities for analyzing normalized B-factors in SBDD are also discussed.
Collapse
Affiliation(s)
- Ted W. Johnson
- Oncology Medicinal Sciences, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Rebecca A. Gallego
- Oncology Medicinal Sciences, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Alexei Brooun
- Oncology Medicinal Sciences, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Dan Gehlhaar
- Oncology Medicinal Sciences, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Michele McTigue
- Oncology Medicinal Sciences, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| |
Collapse
|
5
|
Carugo O. How large B-factors can be in protein crystal structures. BMC Bioinformatics 2018; 19:61. [PMID: 29471780 PMCID: PMC5824579 DOI: 10.1186/s12859-018-2083-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/20/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. RESULTS A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. CONCLUSIONS It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.
Collapse
Affiliation(s)
- Oliviero Carugo
- Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria.
- Department of Chemistry, University of Pavia, viale Taramelli 12, I-27100, Pavia, Italy.
| |
Collapse
|
6
|
Touw WG, Vriend G. BDB: Databank of PDB files with consistent B-factors. Protein Eng Des Sel 2014; 27:457-62. [DOI: 10.1093/protein/gzu044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
7
|
Schmidtke P, Luque FJ, Murray JB, Barril X. Shielded Hydrogen Bonds as Structural Determinants of Binding Kinetics: Application in Drug Design. J Am Chem Soc 2011; 133:18903-10. [DOI: 10.1021/ja207494u] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Schmidtke
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - F. Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - James B. Murray
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom
| | - Xavier Barril
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
8
|
Butler KT, Luque FJ, Barril X. Toward accurate relative energy predictions of the bioactive conformation of drugs. J Comput Chem 2009; 30:601-10. [PMID: 18711721 DOI: 10.1002/jcc.21087] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol(-1) of a local minimum, with penalties above 2.0 kcal mol(-1) being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery.
Collapse
Affiliation(s)
- Keith T Butler
- Institut de Biomedicina de la Universitat de Barcelona & Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | | | | |
Collapse
|
9
|
Parthasarathy S, Murthy MR. Protein thermal stability: insights from atomic displacement parameters (B values). PROTEIN ENGINEERING 2000; 13:9-13. [PMID: 10679524 DOI: 10.1093/protein/13.1.9] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The factors contributing to the thermal stability of proteins from thermophilic origins are matters of intense debate and investigation. Thermophilic proteins are thought to possess better packed interiors than their mesophilic counterparts, leading to lesser overall flexibility and a corresponding reduction in surface-to-volume ratio. These observations prompted an analysis of B values reported in high-resolution X-ray crystal structures of mesophilic and thermophilic proteins. In this analysis, the following aspects were addressed: (1) frequency distribution of normalized B values (B' factors) over all the proteins and for individual amino acids; (2) amino acid compositions in high B value regions of polypeptide chains; (3) variation in the B values from core to the surface of proteins in terms of their radius of gyration; and (4) degree of dispersion of normalized B values in spheres around the Calpha atoms. The analysis revealed that (1) Ser and Thr have lesser flexibility in thermophiles than in mesophiles, (2) the proportion of Glu and Lys in high B value regions of thermophiles is higher and that of Ser and Thr is lower and (3) the dispersion of B values within spheres at Calpha atoms is similar in mesophiles and thermophiles. These observations reflect plausible differences in the dynamics of thermophilic and mesophilic proteins and suggest amino acid substitutions that are likely to change thermal stability.
Collapse
Affiliation(s)
- S Parthasarathy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | |
Collapse
|