1
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Coleman T, Shin J, Silberg JJ, Shamoo Y, Atkinson JT. The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation. Biochemistry 2024; 63:599-609. [PMID: 38357768 DOI: 10.1021/acs.biochem.3c00605] [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: 02/16/2024]
Abstract
Adenylate kinases (AKs) have evolved AMP-binding and lid domains that are encoded as continuous polypeptides embedded at different locations within the discontinuous polypeptide encoding the core domain. A prior study showed that AK homologues of different stabilities consistently retain cellular activity following circular permutation that splits a region with high energetic frustration within the AMP-binding domain into discontinuous fragments. Herein, we show that mesophilic and thermophilic AKs having this topological restructuring retain activity and substrate-binding characteristics of the parental AK. While permutation decreased the activity of both AK homologues at physiological temperatures, the catalytic activity of the thermophilic AK increased upon permutation when assayed >30 °C below the melting temperature of the native AK. The thermostabilities of the permuted AKs were uniformly lower than those of native AKs, and they exhibited multiphasic unfolding transitions, unlike the native AKs, which presented cooperative thermal unfolding. In addition, proteolytic digestion revealed that permutation destabilized each AK in differing manners, and mass spectrometry suggested that the new termini within the AMP-binding domain were responsible for the increased proteolysis sensitivity. These findings illustrate how changes in contact order can be used to tune enzyme activity and alter folding dynamics in multidomain enzymes.
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Affiliation(s)
- Tom Coleman
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - John Shin
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, MS-362, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T Atkinson
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90007, United States
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey 08544, United States
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2
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Liu Z, Thirumalai D. Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology. ACS CENTRAL SCIENCE 2022; 8:763-774. [PMID: 35756371 PMCID: PMC9228575 DOI: 10.1021/acscentsci.2c00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 06/15/2023]
Abstract
Although a large percentage of eukaryotic proteomes consist of proteins with multiple domains, not much is known about their assembly mechanism, especially those with intricate native state architectures. Some have a complex topology in which the structural elements along the sequence are interwoven in such a manner that the domains cannot be separated by cutting at any location along the sequence. Such proteins are multiply connected multidomain proteins (MMPs) with the three-domain (NMP, LID, and CORE) phosphotransferase enzyme adenylate kinase (ADK) being an example. We devised a coarse-grained model to simulate ADK folding initiated by changing either the temperature or guanidinium chloride (GdmCl) concentration. The simulations reproduce the experimentally measured melting temperatures (associated with two equilibrium transitions), FRET efficiency as a function of GdmCl concentration, and the folding times quantitatively. Although the NMP domain orders independently, cooperative interactions between the LID and the CORE domains are required for complete assembly of the enzyme. Kinetic simulations show that, on the collapse time scale, multiple interconnected metastable states are populated, attesting to the folding heterogeneity. The network of kinetically connected states reveals that the CORE domain folds only after the NMP and LID domains, reflecting the interwoven nature of the chain topology.
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Affiliation(s)
- Zhenxing Liu
- Department
of Physics, Beijing Normal University, Beijing 100875, China
| | - D. Thirumalai
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United
States
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3
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The folding and misfolding mechanisms of multidomain proteins. MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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4
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Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020; 9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023] Open
Abstract
The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to ‘U-shaped’ DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4–DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
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5
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Vignesh R, Aradhyam GK. A Change in Domain Cooperativity Drives the Function of Calnuc. Biochemistry 2020; 59:2507-2517. [PMID: 32543177 DOI: 10.1021/acs.biochem.0c00207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
With the increasing incidence of neurodegenerative disorders, there is an urgent need to understand the protein folding process. Examining the folding process of multidomain proteins remains a prime challenge, as their complex conformational dynamics make them highly susceptible to misfolding and/or aggregation. The presence of multiple domains in a protein can lead to interaction between the partially folded domains, thereby driving misfolding and/or aggregation. Calnuc is one such multidomain protein for which Ca2+ binding plays a pivotal role in governing its structural dynamics and stability and, presumably, in directing its interactions with other proteins. We demonstrate differential structural dynamics between the Ca2+-free and Ca2+-bound forms of calnuc. In the absence of Ca2+, full-length calnuc displays equilibrium structural transitions with four intermediate states, reporting a sum of the behavioral properties of its individual domains. Fragment-based studies illustrate the sequential events of structure adoption proceeding in the following order: EF domain followed by the NT and LZ domains in the apo state. On the other hand, Ca2+ binding increases domain cooperativity and enables the protein to fold as a single unit. Single-tryptophan mutant proteins, designed in a domain-dependent manner, confirm an increase in the number of interdomain interactions in the Ca2+-bound form as compared to the Ca2+-free state of the protein, thereby providing insight into its folding process. The attenuated domain crosstalk in apo-calnuc is likely to influence and regulate its physiologically important intermolecular interactions.
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Affiliation(s)
- Ravichandran Vignesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Gopala Krishna Aradhyam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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6
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Bigman LS, Levy Y. Proteins: molecules defined by their trade-offs. Curr Opin Struct Biol 2020; 60:50-56. [DOI: 10.1016/j.sbi.2019.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
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7
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Gershenson A, Gosavi S, Faccioli P, Wintrode PL. Successes and challenges in simulating the folding of large proteins. J Biol Chem 2020; 295:15-33. [PMID: 31712314 PMCID: PMC6952611 DOI: 10.1074/jbc.rev119.006794] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Gō and related structure-based models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003.
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065, India.
| | - Pietro Faccioli
- Dipartimento di Fisica, Universitá degli Studi di Trento, 38122 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201.
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8
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Abstract
This Feature Article presents a view of the protein folding transition based on the hypothesis that Nature has built features within the sequences that enable a Shortcut to efficient folding. Nature's Shortcut is proposed to be the early establishment of a set of nonlocal weak contacts, constituting protein loops that significantly constrain regions of the collapsed disordered protein into a native-like low-resolution fluctuating topology of major sections of the backbone. Nature's establishment of this scaffold of nonlocal contacts is claimed to bypass what would otherwise be a nearly hopeless unaided search for the final three-dimensional structure in proteins longer than ∼100 amino acids. To support this main contention of the Feature Article, the loop hypothesis (LH) description of early folding events is experimentally tested with time-resolved Förster resonance energy transfer techniques for adenylate kinase, and the data are shown to be consistent with theoretical predictions from the sequential collapse model (SCM). The experimentally based LH and the theoretically founded SCM are argued to provide a unified picture of the role of nonlocal contacts as constituting Nature's Shortcut to protein folding. Importantly, the SCM is shown to reliably predict key nonlocal contacts utilizing only primary sequence information. This view on Nature's Shortcut is open to the protein community for further detailed assessment, including its practical consequences, by suitable application of advanced experimental and computational techniques.
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Affiliation(s)
| | - Elisha Haas
- The Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat Gan 52900 , Israel
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9
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Bigman LS, Levy Y. Stability Effects of Protein Mutations: The Role of Long-Range Contacts. J Phys Chem B 2018; 122:11450-11459. [DOI: 10.1021/acs.jpcb.8b07379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lavi S. Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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10
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Kantaev R, Riven I, Goldenzweig A, Barak Y, Dym O, Peleg Y, Albeck S, Fleishman SJ, Haran G. Manipulating the Folding Landscape of a Multidomain Protein. J Phys Chem B 2018; 122:11030-11038. [DOI: 10.1021/acs.jpcb.8b04834] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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11
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The features that distinguish lichenases from other polysaccharide-hydrolyzing enzymes and the relevance of lichenases for biotechnological applications. Appl Microbiol Biotechnol 2018; 102:3951-3965. [DOI: 10.1007/s00253-018-8904-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/16/2023]
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12
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Mazal H, Aviram H, Riven I, Haran G. Effect of ligand binding on a protein with a complex folding landscape. Phys Chem Chem Phys 2018; 20:3054-3062. [PMID: 28721412 DOI: 10.1039/c7cp03327c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG0, due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins. In the current work we studied the effect of ligand binding on the stability of the multi-domain protein adenylate kinase from E. coli (AKE). Unfolding experiments were conducted using single-molecule FRET spectroscopy, which allowed us to directly obtain the fraction of unfolded protein in a model-free way from FRET efficiency histograms. Surprisingly, it was found that the effect of two inhibitors (Ap5A and AMPPNP) and a substrate (AMP) on the stability of AKE was much smaller than expected based on Kd values obtained independently using microscale thermophoresis. To shed light on this issue, we measured the Kd for Ap5A over a range of chemical denaturant concentrations where the protein is still folded. It was found that Kd increases dramatically over this range, likely due to the population of folding intermediates, whose binding to the ligand is much weaker than that of the native state. We propose that binding to folding intermediates may dominate the effect of ligands on the stability of multi-domain proteins, and could therefore have a strong impact on protein homeostasis in vivo.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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13
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Blacklock KM, Yang L, Mulligan VK, Khare SD. A computational method for the design of nested proteins by loop-directed domain insertion. Proteins 2018; 86:354-369. [PMID: 29250820 DOI: 10.1002/prot.25445] [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: 07/24/2017] [Revised: 12/04/2017] [Accepted: 12/15/2017] [Indexed: 12/23/2022]
Abstract
The computational design of novel nested proteins-in which the primary structure of one protein domain (insert) is flanked by the primary structure segments of another (parent)-would enable the generation of multifunctional proteins. Here we present a new algorithm, called Loop-Directed Domain Insertion (LooDo), implemented within the Rosetta software suite, for the purpose of designing nested protein domain combinations connected by flexible linker regions. Conformational space for the insert domain is sampled using large libraries of linker fragments for linker-to-parent domain superimposition followed by insert-to-linker superimposition. The relative positioning of the two domains (treated as rigid bodies) is sampled efficiently by a grid-based, mutual placement compatibility search. The conformations of the loop residues, and the identities of loop as well as interface residues, are simultaneously optimized using a generalized kinematic loop closure algorithm and Rosetta EnzymeDesign, respectively, to minimize interface energy. The algorithm was found to consistently sample near-native conformations and interface sequences for a benchmark set of structurally similar but functionally divergent domain-inserted enzymes from the α/β hydrolase superfamily, and discriminates well between native and nonnative conformations and sequences, although loop conformations tended to deviate from the native conformations. Furthermore, in cross-domain placement tests, native insert-parent domain combinations were ranked as the best-scoring structures compared to nonnative domain combinations. This algorithm should be broadly applicable to the design of multi-domain protein complexes with any combination of inserted or tandem domain connections.
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Affiliation(s)
- Kristin M Blacklock
- Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
| | - Lu Yang
- Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
| | - Vikram K Mulligan
- Institute for Protein Design and Department of Biochemistry, University of Washington, Seattle, Washington
| | - Sagar D Khare
- Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
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14
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Mehaffey MR, Cammarata MB, Brodbelt JS. Tracking the Catalytic Cycle of Adenylate Kinase by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2018; 90:839-846. [PMID: 29188992 PMCID: PMC5750083 DOI: 10.1021/acs.analchem.7b03591] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complex interplay of dynamic protein plasticity and specific side-chain interactions with substrate molecules that allows enzymes to catalyze reactions has yet to be fully unraveled. Top-down ultraviolet photodissociation (UVPD) mass spectrometry is used to track snapshots of conformational fluctuations in the phosphotransferase adenylate kinase (AK) throughout its active reaction cycle by characterization of complexes containing AK and each of four different adenosine phosphate ligands. Variations in efficiencies of UVPD backbone cleavages were consistently observed for three α-helices and the adenosine binding regions for AK complexes representing different steps of the catalytic cycle, implying that these stretches of the protein sample various structural microstates as the enzyme undergoes global open-to-closed transitions. Focusing on the conformational impact of recruiting or releasing the Mg2+ cofactor highlights two loop regions for which fragmentation increases upon UVPD, signaling an increase in loop flexibility as the metal cation disrupts the loop interactions with the substrate ligands. Additionally, the observation of holo ions and variations in UVPD backbone cleavage efficiency at R138 implicate this conserved active site residue in stabilizing the donor phosphoryl group during catalysis. This study showcases the utility of UVPD-MS to provide insight into conformational fluctuations of single residues for active enzymes.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
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15
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Bou-Nader C, Pecqueur L, Cornu D, Lombard M, Dezi M, Nicaise M, Velours C, Fontecave M, Hamdane D. Power of protein/tRNA functional assembly against aberrant aggregation. Phys Chem Chem Phys 2017; 19:28014-28027. [PMID: 29034944 DOI: 10.1039/c7cp05599d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the mechanisms of protein oligomerization and aggregation is a major concern for biotechnology and medical purposes. However, significant challenges remain in determining the mechanism of formation of these superstructures and the environmental factors that can precisely modulate them. Notably the role that a functional ligand plays in the process of protein aggregation is largely unexplored. We herein address these issues with an original flavin-dependent RNA methyltransferase (TrmFO) used as a protein model since this protein employs a complex set of cofactors and ligands for catalysis. Here, we show that TrmFO carries an unstable protein structure that can partially mis-unfold leading to either formation of irregular and nonfunctional soluble oligomers endowed with hyper-thermal stability or large amorphous aggregates in the presence of salts. Mutagenesis confirmed that this peculiarity is an intrinsic property of a polypeptide and it is independent of the flavin coenzyme. Structural characterization and kinetic studies identified several regions of the protein that enjoy conformational changes and more particularly pinpointed the N-terminal subdomain as being a key element in the mechanisms of oligomerization and aggregation. Only stabilization of this region via tRNA suppresses these aberrant protein states. Although protein chaperones emerged as major actors against aggregation, our study emphasizes that other powerful mechanisms exist such as the stabilizing effect of functional assemblies that provide an additional layer of protection against the instability of the proteome.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France.
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16
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Schön A, Clarkson BR, Jaime M, Freire E. Temperature stability of proteins: Analysis of irreversible denaturation using isothermal calorimetry. Proteins 2017; 85:2009-2016. [PMID: 28722205 DOI: 10.1002/prot.25354] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 01/17/2023]
Abstract
The structural stability of proteins has been traditionally studied under conditions in which the folding/unfolding reaction is reversible, since thermodynamic parameters can only be determined under these conditions. Achieving reversibility conditions in temperature stability experiments has often required performing the experiments at acidic pH or other nonphysiological solvent conditions. With the rapid development of protein drugs, the fastest growing segment in the pharmaceutical industry, the need to evaluate protein stability under formulation conditions has acquired renewed urgency. Under formulation conditions and the required high protein concentration (∼100 mg/mL), protein denaturation is irreversible and frequently coupled to aggregation and precipitation. In this article, we examine the thermal denaturation of hen egg white lysozyme (HEWL) under irreversible conditions and concentrations up to 100 mg/mL using several techniques, especially isothermal calorimetry which has been used to measure the enthalpy and kinetics of the unfolding and aggregation/precipitation at 12°C below the transition temperature measured by DSC. At those temperatures the rate of irreversible protein denaturation and aggregation of HEWL is measured to be on the order of 1 day-1 . Isothermal calorimetry appears a suitable technique to identify buffer formulation conditions that maximize the long term stability of protein drugs.
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Affiliation(s)
- Arne Schön
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Benjamin R Clarkson
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Maria Jaime
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Ernesto Freire
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
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17
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Halder R, Manna RN, Chakraborty S, Jana B. Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π–Cation Interaction. J Phys Chem B 2017; 121:5699-5708. [DOI: 10.1021/acs.jpcb.7b01736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rabindra Nath Manna
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sandipan Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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18
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Coarse-grained models for studying protein diffusion along DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1262] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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19
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Cui D, Ren W, Li W, Wang W. Molecular simulations of substrate release and coupled conformational motions in adenylate kinase. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Conformational opening coupled substrate release is believed to be related to the rate limiting step in the catalysis cycle of the adenylate kinase. However, it is still unclear how the substrate dissociates from its active site and how the substrate release is coupled to conformational changes of the kinase. In this work, by using metadynamics simulations, we investigated the ADP release process and the coupled protein dynamics. We found that the ADP release involves overcoming a high free energy barrier, and protonation of the [Formula: see text]-phosphate of the ADP molecules can drastically reduce the barrier height, therefore, promote the ADP release. We identified several key residues contributing to the high free energy barrier. We also showed that the ADP attached to LID domain leaves the binding pocket earlier than the one attached to the NMP domain. We further observed that the ADP release is accompanied by almost fully opening of the LID domain and partially opening of the NMP domain. Our results provide insight into the molecular mechanism of the substrate release of adenylate kinase and the coupled conformational motions.
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Affiliation(s)
- Dachao Cui
- Department of Physics, Nanjing University, Nanjing 210093, P. R. China
| | - Weitong Ren
- Department of Physics, Nanjing University, Nanjing 210093, P. R. China
| | - Wenfei Li
- Department of Physics, Nanjing University, Nanjing 210093, P. R. China
| | - Wei Wang
- Department of Physics, Nanjing University, Nanjing 210093, P. R. China
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20
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Using the folding landscapes of proteins to understand protein function. Curr Opin Struct Biol 2016; 36:67-74. [PMID: 26812092 DOI: 10.1016/j.sbi.2016.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/31/2015] [Accepted: 01/06/2016] [Indexed: 11/20/2022]
Abstract
Proteins fold on a biologically-relevant timescale because of a funnel-shaped energy landscape. This landscape is sculpted through evolution by selecting amino-acid sequences that stabilize native interactions while suppressing stable non-native interactions that occur during folding. However, there is strong evolutionary selection for functional residues and these cannot be chosen to optimize folding. Their presence impacts the folding energy landscape in a variety of ways. Here, we survey the effects of functional residues on folding by providing several examples. We then review how such effects can be detected computationally and be used as assays for protein function. Overall, an understanding of how functional residues modulate folding should provide insights into the design of natural proteins and their homeostasis.
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He E, Ren W, Wang J, Li W, Wang W. Effects of heme binding on myoglobin folding: Coarse grained molecular simulations. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633615500595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Many proteins contain cofactors, such as heme, ATP and metal ions. Binding of cofactors is not only essential for their biological functions, but also can reshape the intrinsic energy landscape of protein molecules and modulate the folding and stability. However, the molecular mechanism of cofactor coupled protein folding is not well understood. In this work, we study the cofactor coupled folding of myoglobin, which is a typical cofactor (heme) containing protein, by performing molecular dynamics simulations with a structure-based protein model developed based on the energy landscape theory. We showed that the heme binding increases the stability of the myoglobin. More importantly, the heme binding tends to increase the protein folding cooperativity, and switch the folding process from a “three-state” mechanism to a “two-state” mechanism. We also showed that the folding pathways of the myoglobin can be modulated by the heme binding. By performing comparative simulations, we revealed that the above effects of heme binding are resulted from the heme induced folding of F-helix, which is otherwise unstructured at apo state, and the heme mediated contacting interactions around the heme binding site. The simulation results are consistent with available experimental data, and provide insights into the molecular mechanism of the effects of cofactor binding on the protein folding and stability.
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Affiliation(s)
- Erbin He
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Weitong Ren
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Jun Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wei Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
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Watkins A, Wuo MG, Arora PS. Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. J Am Chem Soc 2015; 137:11622-30. [PMID: 26302018 PMCID: PMC4577960 DOI: 10.1021/jacs.5b05527] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 12/26/2022]
Abstract
The modulation of protein-protein interactions (PPIs) by means of creating or stabilizing secondary structure conformations is a rapidly growing area of research. Recent success in the inhibition of difficult PPIs by secondary structure mimetics also points to potential limitations, because often, specific cases require tertiary structure mimetics. To streamline protein structure-based inhibitor design, we have previously described the examination of protein complexes in the Protein Data Bank where α-helices or β-strands form critical contacts. Here, we examined coiled coils and helix bundles that mediate complex formation to create a platform for the discovery of potential tertiary structure mimetics. Though there has been extensive analysis of coiled coil motifs, the interactions between pre-formed coiled coils and globular proteins have not been systematically analyzed. This article identifies critical features of these helical interfaces with respect to coiled coil and other helical PPIs. We expect the analysis to prove useful for the rational design of modulators of this fundamental class of protein assemblies.
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Affiliation(s)
- Andrew
M. Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Michael G. Wuo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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Gavrilov Y, Hagai T, Levy Y. Nonspecific yet decisive: Ubiquitination can affect the native-state dynamics of the modified protein. Protein Sci 2015; 24:1580-92. [PMID: 25970168 DOI: 10.1002/pro.2688] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/05/2015] [Indexed: 11/10/2022]
Abstract
Ubiquitination is one of the most common post-translational modifications of proteins, and mediates regulated protein degradation among other cellular processes. A fundamental question regarding the mechanism of protein ubiquitination is whether and how ubiquitin affects the biophysical nature of the modified protein. For some systems, it was shown that the position of ubiquitin within the attachment site is quite flexible and ubiquitin does not specifically interact with its substrate. Nevertheless, it was revealed that polyubiquitination can decrease the thermal stability of the modified protein in a site-specific manner because of alterations of the thermodynamic properties of the folded and unfolded states. In this study, we used detailed atomistic simulations to focus on the molecular effects of ubiquitination on the native structure of the modified protein. As a model, we used Ubc7, which is an E2 enzyme whose in vivo ubiquitination process is well characterized and known to lead to degradation. We found that, despite the lack of specific direct interactions between the ubiquitin moiety and Ubc7, ubiquitination decreases the conformational flexibility of certain regions of the substrate Ubc7 protein, which reduces its entropy and thus destabilizes it. The strongest destabilizing effect was observed for systems in which Lys48-linked tetra-ubiquitin was attached to sites used for in vivo degradation. These results reveal how changes in the configurational entropy of the folded state may modulate the stability of the protein's native state. Overall, our results imply that ubiquitination can modify the biophysical properties of the attached protein in the folded state and that, in some proteins, different ubiquitination sites will lead to different biophysical outcomes. We propose that this destabilizing effect of polyubiquitin on the substrate is linked to the functions carried out by the modification, and in particular, regulatory control of protein half-life through proteasomal degradation.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Tzachi Hagai
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
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