1
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Kumar M, Rathore RS. Disallowed spots in protein structures. Biochim Biophys Acta Gen Subj 2023; 1867:130493. [PMID: 37865175 DOI: 10.1016/j.bbagen.2023.130493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 10/23/2023]
Abstract
Ramachandran (ϕ, ψ) steric map was introduced in 1963 to describe available conformation space for protein structures. Subsequently, residues were observed in high-energy disallowed regions of the map. To unequivocally identify the locations of disallowed conformations of residues, we got 36 noise-free protein structures (resolution ≤1 Å, Rwork/Rfree ≤ 0.10). These stringent criteria were applied to rule out data or model errors or any crystallographic disorders. No disallowed conformation was found in the dataset. Further, we also examined disallowed conformations in a larger dataset (resolution ≤1.5 Å, devoid of any model errors, or disorders). The observed locations of disallowed residues are referred as disallowed spots. These spots include short loops of 3-5 residues, and locations where residues participate in disulfide bonding or intramolecular interactions or inter-molecular interactions with neighboring water, metals or ligands. Conformational sampling revealed that short loops in between secondary structures hardly have any opportunity to relieve from conformational strain. Residues involved in interactions, which provide energetic compensation for high-energy conformational states, were relieved from strain once the causative interaction was removed. The present study aims to identify disallowed spots in the native state of proteins, wherein residues are forced to be trapped in high-energy disallowed conformations. Moreover, it was also observed that pre-Pro, Ser, Asp, trans-Pro, Val, Asn & Gly have higher tendency to occur in disallowed conformation, which could be attributed to factors such as conformational restrictions, residue propensity of secondary structures and compensating sidechain and mainchain interactions, stabilizing turn-mimics.
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Affiliation(s)
- Mayank Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India
| | - R S Rathore
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India.
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2
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Diaz DB, Appavoo SD, Bogdanchikova AF, Lebedev Y, McTiernan TJ, Dos Passos Gomes G, Yudin AK. Illuminating the dark conformational space of macrocycles using dominant rotors. Nat Chem 2021; 13:218-225. [PMID: 33589789 DOI: 10.1038/s41557-020-00620-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Three-dimensional conformation is the primary determinant of molecular properties. The thermal energy available at room temperature typically equilibrates the accessible conformational states. Here, we introduce a method for isolating unique and previously understudied conformations of macrocycles. The observation of unusual conformations of 16- to 22-membered rings has been made possible by controlling their interconversion using dominant rotors, which represent tunable atropisomeric constituents with relatively high rotational barriers. Density functional theory and in situ NMR measurements suggest that dominant rotor candidates for the amino-acid-based structures considered here should possess a rotational energy barrier of at least 25 kcal mol-1. Notable differences in the geometries of the macrocycle conformations were identified by NMR spectroscopy and X-ray crystallography. There is evidence that amino acid residues can be forced into rare turn motifs not observed in the corresponding linear counterparts and homodetic rings. These findings should unlock new avenues for studying the conformation-activity relationships of bioactive molecules.
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Affiliation(s)
- Diego B Diaz
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Solomon D Appavoo
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Yury Lebedev
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Gabriel Dos Passos Gomes
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Andrei K Yudin
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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3
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Tronrud DE, Karplus PA. A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins. Acta Crystallogr D Struct Biol 2021; 77:249-266. [DOI: 10.1107/s2059798320016344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
While broadening the applicability of (φ/ψ)-dependent target values for the bond angles in the peptide backbone, sequence/conformation categories with too few residues to analyze via previous methods were encountered. Here, a method of describing a conformation-dependent library (CDL) using two-dimensional Fourier coefficients is reported where the number of coefficients for individual categories is determined via complete cross-validation. Sample sizes are increased further by selective blending of categories with similar patterns of conformational dependence. An additional advantage of the Fourier-synthesis-based CDL is that it uses continuous functions and has no artifactual steps near the edges of populated regions of φ/ψ space. A set of libraries for the seven main-chain bond angles, along with the ω and ζ angles, was created based on a set of Fourier analyses of 48 368 residues selected from high-resolution models in the wwPDB. This new library encompasses both trans- and cis-peptide bonds and outperforms currently used discrete CDLs.
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4
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Xu X, Gagné D, Aramini JM, Gardner KH. Volume and compressibility differences between protein conformations revealed by high-pressure NMR. Biophys J 2021; 120:924-935. [PMID: 33524371 DOI: 10.1016/j.bpj.2020.12.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/25/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Proteins often interconvert between different conformations in ways critical to their function. Although manipulating such equilibria for biophysical study is often challenging, the application of pressure is a potential route to achieve such control by favoring the population of lower volume states. Here, we use this feature to study the interconversion of ARNT PAS-B Y456T, which undergoes a dramatic +3 slip in the β-strand register as it switches between two stably folded conformations. Using high-pressure biomolecular NMR approaches, we obtained the first, to our knowledge, quantitative data testing two key hypotheses of this process: the slipped conformation is both smaller and less compressible than the wild-type equivalent, and the interconversion proceeds through a chiefly unfolded intermediate state. Data collected in steady-state pressure and time-resolved pressure-jump modes, including observed pressure-dependent changes in the populations of the two conformers and increased rate of interconversion between conformers, support both hypotheses. Our work exemplifies how these approaches, which can be generally applied to protein conformational switches, can provide unique information that is not easily accessible through other techniques.
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Affiliation(s)
- Xingjian Xu
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York; Ph.D Program in Biochemistry, The Graduate Center, CUNY, New York, New York
| | - Donald Gagné
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York
| | - James M Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York; Department of Chemistry and Biochemistry, City College of New York, New York, New York; Ph.D. Programs in Biochemistry, Chemistry, and Biology, The Graduate Center, CUNY, New York, New York.
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5
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Rosen MR, Leuthaeuser JB, Parish CA, Fetrow JS. Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters. Biochemistry 2020; 59:4262-4284. [PMID: 33135415 DOI: 10.1021/acs.biochem.0c00651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs). Broad superfamily classifications align with redox partners (Trx- or Grx-linked). To understand this superfamily's mechanistic diversity, the ArsC superfamily is classified on the basis of active site features utilizing the tools TuLIP (two-level iterative clustering process) and autoMISST (automated multilevel iterative sequence searching technique). This approach identified nine functionally relevant (perhaps isofunctional) protein groups. Five groups exhibit distinct ArsC mechanisms. Three are Grx-linked: group 4AA (classical ArsC), group 3AAA (YffB-like), and group 5BAA. Two are Trx-linked: groups 6AAAAA and 7AAAAAAAA. One is an Spx-like transcriptional regulatory group, group 5AAA. Three are potential LMW-PTP groups: groups 7BAAAA, and 7AAAABAA, which have not been previously identified, and the well-studied LMW-PTP family group 8AAA. Molecular dynamics simulations were utilized to explore functional site details. In several families, we confirm and add detail to literature-based mechanistic information. Mechanistic roles are hypothesized for conserved active site residues in several families. In three families, simulations of the unliganded structure sample specific conformational ensembles, which are proposed to represent either a more ligand-binding-competent conformation or a pathway toward a more binding-competent state; these active sites may be designed to traverse high-energy barriers to the lower-energy conformations necessary to more readily bind ligands. This more detailed biochemical understanding of ArsC and ArsC-like PTP mechanisms opens possibilities for further understanding of arsenate bioremediation and the LMW-PTP mechanism.
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Affiliation(s)
- Mikaela R Rosen
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Janelle B Leuthaeuser
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Carol A Parish
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Jacquelyn S Fetrow
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
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6
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Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis. Proc Natl Acad Sci U S A 2019; 116:25634-25640. [PMID: 31801874 DOI: 10.1073/pnas.1901864116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.
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7
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Jiang Z, Biczysko M, Moriarty NW. Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations. Proteins 2018; 86:273-278. [DOI: 10.1002/prot.25451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/16/2017] [Accepted: 01/01/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Zhongming Jiang
- International Centre for Quantum and Molecular Structures, College of Sciences; Shanghai University, 99 Shangda Road; 200444 Shanghai China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, College of Sciences; Shanghai University, 99 Shangda Road; 200444 Shanghai China
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division; Lawrence Berkeley National Laboratory; Berkeley California 94720
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Bottaro S, Gil-Ley A, Bussi G. RNA folding pathways in stop motion. Nucleic Acids Res 2016; 44:5883-91. [PMID: 27091499 PMCID: PMC4937309 DOI: 10.1093/nar/gkw239] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/29/2016] [Accepted: 03/29/2016] [Indexed: 11/19/2022] Open
Abstract
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions.
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Affiliation(s)
- Sandro Bottaro
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy
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Gil-Ley A, Bottaro S, Bussi G. Empirical Corrections to the Amber RNA Force Field with Target Metadynamics. J Chem Theory Comput 2016; 12:2790-8. [PMID: 27153317 PMCID: PMC4910146 DOI: 10.1021/acs.jctc.6b00299] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 11/30/2022]
Abstract
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the α and ζ backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement.
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Affiliation(s)
- Alejandro Gil-Ley
- Scuola
Internazionale Superiore
di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Sandro Bottaro
- Scuola
Internazionale Superiore
di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola
Internazionale Superiore
di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
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Brereton AE, Karplus PA. On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures. Protein Sci 2016; 25:926-32. [PMID: 26779991 PMCID: PMC4941219 DOI: 10.1002/pro.2883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/11/2016] [Indexed: 11/06/2022]
Abstract
Ultra-high resolution protein crystal structures have been considered as relatively reliable sources for defining details of protein geometry, such as the extent to which the peptide unit deviates from planarity. Chellapa and Rose (Proteins 2015; 83:1687) recently called this into question, reporting that for a dozen representative protein structures determined at ∼ 1 Å resolution, the diffraction data could be equally well fit with models restrained to have highly planar peptides, i.e. having a standard deviation of the ω torsion angles of only ∼ 1° instead of the typically observed value of ∼ 6°. Here, we document both conceptual and practical shortcomings of that study and show that the more tightly restrained models are demonstrably incorrect and do not fit the diffraction data equally well. We emphasize the importance of inspecting electron density maps when investigating the agreement between a model and its experimental data. Overall, this report reinforces that modern standard refinement protocols have been well-conceived and that ultra-high resolution protein crystal structures, when evaluated carefully and used with an awareness of their levels of coordinate uncertainty, are powerful sources of information for providing reliable information about the details of protein geometry.
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Affiliation(s)
- Andrew E. Brereton
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallis97331Oregon
| | - P. Andrew Karplus
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallis97331Oregon
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