1
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Caetano DLZ, Metzler R, Cherstvy AG, de Carvalho SJ. Adsorption of lysozyme into a charged confining pore. Phys Chem Chem Phys 2021; 23:27195-27206. [PMID: 34821240 DOI: 10.1039/d1cp03185f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Several applications arise from the confinement of proteins on surfaces because their stability and biological activity are enhanced. It is also known that the way in which a protein adsorbs on the surface is important for its biological function since its active sites should not be obstructed. In this study, the adsorption properties of hen egg-white lysozyme, HEWL, into a negatively charged silica pore is examined by employing a coarse-grained model and constant-pH Monte Carlo simulations. The role of electrostatic interactions is taken into account via including the Debye-Hückel potentials into the Cα structure-based model. We evaluate the effects of pH, salt concentration, and pore radius on the protein preferential orientation and spatial distribution of its residues regarding the pore surface. By mapping the residues that stay closer to the pore surface, we find that the increase of pH leads to orientational changes of the adsorbed protein when the solution pH gets closer to the HEWL isoelectric point. Under these conditions, the pKa shift of these important residues caused by the adsorption into the charged confining surface results in a HEWL charge distribution that stabilizes the adsorption in the observed protein orientation. We compare our observations to the results of the pKa shift for HEWL available in the literature and to some experimental data.
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Affiliation(s)
- Daniel L Z Caetano
- Institute of Chemistry, State University of Campinas (UNICAMP), Campinas, Brazil.,Center for Computational Engineering and Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.,Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Sidney J de Carvalho
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, Brazil.
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2
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Wruck F, Tian P, Kudva R, Best RB, von Heijne G, Tans SJ, Katranidis A. The ribosome modulates folding inside the ribosomal exit tunnel. Commun Biol 2021; 4:523. [PMID: 33953328 PMCID: PMC8100117 DOI: 10.1038/s42003-021-02055-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/29/2021] [Indexed: 12/16/2022] Open
Abstract
Proteins commonly fold co-translationally at the ribosome, while the nascent chain emerges from the ribosomal exit tunnel. Protein domains that are sufficiently small can even fold while still located inside the tunnel. However, the effect of the tunnel on the folding dynamics of these domains is not well understood. Here, we combine optical tweezers with single-molecule FRET and molecular dynamics simulations to investigate folding of the small zinc-finger domain ADR1a inside and at the vestibule of the ribosomal tunnel. The tunnel is found to accelerate folding and stabilize the folded state, reminiscent of the effects of chaperonins. However, a simple mechanism involving stabilization by confinement does not explain the results. Instead, it appears that electrostatic interactions between the protein and ribosome contribute to the observed folding acceleration and stabilization of ADR1a.
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Affiliation(s)
- Florian Wruck
- AMOLF, Amsterdam, The Netherlands.,Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Pengfei Tian
- Protein Engineering, Novozymes A/S, Lyngby, Denmark
| | - Renuka Kudva
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Sander J Tans
- AMOLF, Amsterdam, The Netherlands. .,Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands. .,Kavli Institute of Nanoscience, Delft, The Netherlands.
| | - Alexandros Katranidis
- Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich (FZJ), Jülich, Germany.
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3
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Bergman O, Karry R, Milhem J, Ben-Shachar D. NDUFV2 pseudogene (NDUFV2P1) contributes to mitochondrial complex I deficits in schizophrenia. Mol Psychiatry 2020; 25:805-820. [PMID: 30531937 DOI: 10.1038/s41380-018-0309-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria together with other cellular components maintain a constant crosstalk, modulating transcriptional and posttranslational processes. We and others demonstrated mitochondrial multifaceted dysfunction in schizophrenia, with aberrant complex I (CoI) as a major cause. Here we show deficits in CoI activity and homeostasis in schizophrenia-derived cell lines. Focusing on a core CoI subunit, NDUFV2, one of the most severely affected subunits in schizophrenia, we observed reduced protein level and functioning, with no change in mRNA transcripts. We further show that NDUFV2 pseudogene (NDUFV2P1) expression is increased in schizophrenia-derived cells and in postmortem brain specimens. In schizophrenia and controls pooled samples, NDUFV2P1 level demonstrated a significant inverse correlation with NDUFV2 pre- and matured protein level and with CoI-driven cellular respiration. Our data suggest a role for a pseudogene in its parent-gene regulation and possibly in CoI dysfunction in schizophrenia. The abnormal expression of the pseudogene may be one element of a vicious circle in which CoI deficits lead to mitochondrial dysfunction potentially affecting genome-wide regulation of gene expression, including the expression of pseudogenes.
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Affiliation(s)
- Oded Bergman
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rachel Karry
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Jumana Milhem
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dorit Ben-Shachar
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, B. Rappaport Faculty of Medicine and Rappaport Family Institute for Research in Medical Sciences, Technion-Israel Institute of Technology, Haifa, Israel.
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4
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Kang C, Keller TH. Probing biological mechanisms with chemical tools. Pharmacol Res 2020; 153:104656. [PMID: 31962154 DOI: 10.1016/j.phrs.2020.104656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/09/2020] [Accepted: 01/17/2020] [Indexed: 12/19/2022]
Abstract
Traditionally small molecules have mainly been used to inhibit biochemical activities of proteins, however such compounds can also be used to change the conformational energy landscape of proteins. Tool compounds that modulate protein conformations often reveal unexpected biological mechanisms, which have therapeutic potential. We discuss two examples where screening hits were found to bind to unexpected binding pockets on well known proteins, establishing new routes for the inhibition of proteins that were thought to be undruggable.
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Affiliation(s)
- Congbao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, 138670, Singapore
| | - Thomas H Keller
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, 138670, Singapore.
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5
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Abstract
Most proteins need to fold into a specific 3D structure to function. The mechanism by which isolated proteins fold has been thoroughly studied by experiment and theory. However, in the cell proteins do not fold in isolation but are synthesized as linear chains by the ribosome during translation. It is therefore natural to ask at which point during synthesis proteins fold, and whether this differs from the folding of isolated protein molecules. By studying folding of a well-characterized protein domain, titin I27, stalled at different points during translation, we show that it already folds in the mouth of the ribosome exit tunnel and that the mechanism is almost identical to that of the isolated protein. Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-β Ig domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force dependence of escape from arrest accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations—which also reproduce experiments on mutant forms of I27—show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.
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6
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Wang C, Piroozan N, Javidpour L, Sahimi M. Effect of the geometry of confining media on the stability and folding rate of α -helix proteins. J Chem Phys 2018; 148:194305. [PMID: 30307193 DOI: 10.1063/1.5020841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium's walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D 0 is only slightly larger than the smallest dimension of a protein's folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys. 135, 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs in larger pores for smaller α-helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with an α-helical native state that contain the β structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins' misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperature T f on the size D of a confined medium occurs in larger media for larger proteins is correct only in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media's walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium.
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Affiliation(s)
- Congyue Wang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Nariman Piroozan
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Leili Javidpour
- Departments of Energy Engineering and Physics, Amirkabir University of Technology, Tehran 15875-4413, Iran
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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7
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Cheng C, Wu J, Liu G, Shi S, Chen T. Effects of Non-native Interactions on Frustrated Proteins Folding under Confinement. J Phys Chem B 2018; 122:7654-7667. [DOI: 10.1021/acs.jpcb.8b04147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Chenqian Cheng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Jing Wu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Gaoyuan Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Suqing Shi
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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8
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Abstract
The GroEL/ES chaperonin is known to prevent protein aggregation during folding by passive containment within the central cavity. The possible role of more active intervention is controversial. The HX MS method documents an organized hydrophobically stabilized folding preintermediate in the collapsed ensemble of maltose binding protein. A mutational defect destabilizes the preintermediate and greatly slows folding of the subsequent on-pathway H-bonded intermediate. GroEL encapsulation alone, without ATP and substrate protein cycling, restabilizes the preintermediate and restores fast folding. The mechanism appears to depend on forceful compression during confinement. More generally, these results suggest that GroEL can repair different folding defects in different ways. We used hydrogen exchange–mass spectrometry (HX MS) and fluorescence to compare the folding of maltose binding protein (MBP) in free solution and in the GroEL/ES cavity. Upon refolding, MBP initially collapses into a dynamic molten globule-like ensemble, then forms an obligatory on-pathway native-like folding intermediate (1.2 seconds) that brings together sequentially remote segments and then folds globally after a long delay (30 seconds). A single valine to glycine mutation imposes a definable folding defect, slows early intermediate formation by 20-fold, and therefore subsequent global folding by approximately twofold. Simple encapsulation within GroEL repairs the folding defect and reestablishes fast folding, with or without ATP-driven cycling. Further examination exposes the structural mechanism. The early folding intermediate is stabilized by an organized cluster of 24 hydrophobic side chains. The cluster preexists in the collapsed ensemble before the H-bond formation seen by HX MS. The V9G mutation slows folding by disrupting the preintermediate cluster. GroEL restores wild-type folding rates by restabilizing the preintermediate, perhaps by a nonspecific equilibrium compression effect within its tightly confining central cavity. These results reveal an active GroEL function other than previously proposed mechanisms, suggesting that GroEL possesses different functionalities that are able to relieve different folding problems. The discovery of the preintermediate, its mutational destabilization, and its restoration by GroEL encapsulation was made possible by the measurement of a previously unexpected type of low-level HX protection, apparently not dependent on H-bonding, that may be characteristic of proteins in confined spaces.
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9
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Abstract
Markov state models (MSMs) are an extremely useful tool for understanding the conformational dynamics of macromolecules and for analyzing MD simulations in a quantitative fashion. They have been extensively used for peptide and protein folding, for small molecule binding, and for the study of native ensemble dynamics. Here, we adapt the MSM methodology to gain insight into the dynamics of misfolded states. To overcome possible flaws in root-mean-square deviation (RMSD)-based metrics, we introduce a novel discretization approach, based on coarse-grained contact maps. In addition, we extend the MSM methodology to include "sink" states in order to account for the irreversibility (on simulation time scales) of processes like protein misfolding. We apply this method to analyze the mechanism of misfolding of tandem repeats of titin domains, and how it is influenced by confinement in a chaperonin-like cavity.
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Affiliation(s)
- Anshul Sirur
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Robert B Best
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
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10
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Macdonald B, McCarley S, Noeen S, van Giessen AE. β-Hairpin Crowding Agents Affect α-Helix Stability in Crowded Environments. J Phys Chem B 2016; 120:650-9. [DOI: 10.1021/acs.jpcb.5b10575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bryanne Macdonald
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Shannon McCarley
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Sundus Noeen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Alan E. van Giessen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
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11
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Faísca PF. Knotted proteins: A tangled tale of Structural Biology. Comput Struct Biotechnol J 2015; 13:459-68. [PMID: 26380658 PMCID: PMC4556803 DOI: 10.1016/j.csbj.2015.08.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/31/2015] [Accepted: 08/07/2015] [Indexed: 01/19/2023] Open
Abstract
Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.
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12
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Shin J, Cherstvy AG, Metzler R. Polymer Looping Is Controlled by Macromolecular Crowding, Spatial Confinement, and Chain Stiffness. ACS Macro Lett 2015; 4:202-206. [PMID: 35596432 DOI: 10.1021/mz500709w] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We study by extensive computer simulations the looping characteristics of linear polymers with varying persistence length inside a spherical cavity in the presence of macromolecular crowding. For stiff chains, the looping probability and looping time reveal wildly oscillating patterns as functions of the chain length. The effects of crowding differ dramatically for flexible versus stiff polymers. While for flexible chains the looping kinetics is slowed down by the crowders, for stiffer chains the kinetics turns out to be either decreased or facilitated, depending on the polymer length. For severe confinement, the looping kinetics may become strongly facilitated by crowding. Our findings are of broad impact for DNA looping in the crowded and compartmentalized interior of living biological cells.
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Affiliation(s)
- Jaeoh Shin
- Institute
for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Max-Planck Institute
for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Andrey G. Cherstvy
- Institute
for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute
for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Department
of Physics, Tampere University of Technology, 33101 Tampere, Finland
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13
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Macdonald B, McCarley S, Noeen S, van Giessen AE. Protein–Protein Interactions Affect Alpha Helix Stability in Crowded Environments. J Phys Chem B 2015; 119:2956-67. [DOI: 10.1021/jp512630s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Bryanne Macdonald
- Department of Chemistry, Mount Holyoke College, 50 College Street, South
Hadley, Massachusetts 01075, United States
| | - Shannon McCarley
- Department of Chemistry, Mount Holyoke College, 50 College Street, South
Hadley, Massachusetts 01075, United States
| | - Sundus Noeen
- Department of Chemistry, Mount Holyoke College, 50 College Street, South
Hadley, Massachusetts 01075, United States
| | - Alan E. van Giessen
- Department of Chemistry, Mount Holyoke College, 50 College Street, South
Hadley, Massachusetts 01075, United States
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14
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Yadahalli S, Hemanth Giri Rao VV, Gosavi S. Modeling Non-Native Interactions in Designed Proteins. Isr J Chem 2014. [DOI: 10.1002/ijch.201400035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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