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Xu H, Xu D, Liu Y. Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04810-5. [PMID: 38183603 DOI: 10.1007/s12010-023-04810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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2
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Nowak JS, Otzen DE. Helping proteins come in from the cold: 5 burning questions about cold-active enzymes. BBA ADVANCES 2023; 5:100104. [PMID: 38162634 PMCID: PMC10755280 DOI: 10.1016/j.bbadva.2023.100104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/21/2023] [Accepted: 09/05/2023] [Indexed: 01/03/2024] Open
Abstract
Enzymes from psychrophilic (cold-loving) organisms have attracted considerable interest over the past decades for their potential in various low-temperature industrial processes. However, we still lack large-scale commercialization of their activities. Here, we review their properties, limitations and potential. Our review is structured around answers to 5 central questions: 1. How do cold-active enzymes achieve high catalytic rates at low temperatures? 2. How is protein flexibility connected to cold-activity? 3. What are the sequence-based and structural determinants for cold-activity? 4. How does the thermodynamic stability of psychrophilic enzymes reflect their cold-active capabilities? 5. How do we effectively identify novel cold-active enzymes, and can we apply them in an industrial context? We conclude that emerging screening technologies combined with big-data handling and analysis make it reasonable to expect a bright future for our understanding and exploitation of cold-active enzymes.
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Affiliation(s)
- Jan Stanislaw Nowak
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
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3
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Huang Z, Cui X, Xia Y, Zhao K, Zhang G. Pathfinder: Protein folding pathway prediction based on conformational sampling. PLoS Comput Biol 2023; 19:e1011438. [PMID: 37695768 PMCID: PMC10513300 DOI: 10.1371/journal.pcbi.1011438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/21/2023] [Accepted: 08/17/2023] [Indexed: 09/13/2023] Open
Abstract
The study of protein folding mechanism is a challenge in molecular biology, which is of great significance for revealing the movement rules of biological macromolecules, understanding the pathogenic mechanism of folding diseases, and designing protein engineering materials. Based on the hypothesis that the conformational sampling trajectory contain the information of folding pathway, we propose a protein folding pathway prediction algorithm named Pathfinder. Firstly, Pathfinder performs large-scale sampling of the conformational space and clusters the decoys obtained in the sampling. The heterogeneous conformations obtained by clustering are named seed states. Then, a resampling algorithm that is not constrained by the local energy basin is designed to obtain the transition probabilities of seed states. Finally, protein folding pathways are inferred from the maximum transition probabilities of seed states. The proposed Pathfinder is tested on our developed test set (34 proteins). For 11 widely studied proteins, we correctly predicted their folding pathways and specifically analyzed 5 of them. For 13 proteins, we predicted their folding pathways to be further verified by biological experiments. For 6 proteins, we analyzed the reasons for the low prediction accuracy. For the other 4 proteins without biological experiment results, potential folding pathways were predicted to provide new insights into protein folding mechanism. The results reveal that structural analogs may have different folding pathways to express different biological functions, homologous proteins may contain common folding pathways, and α-helices may be more prone to early protein folding than β-strands.
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Affiliation(s)
- Zhaohong Huang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xinyue Cui
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuhao Xia
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Kailong Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
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4
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FK506-Binding Protein 2 Participates in Proinsulin Folding. Biomolecules 2023; 13:biom13010152. [PMID: 36671537 PMCID: PMC9855983 DOI: 10.3390/biom13010152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Apart from chaperoning, disulfide bond formation, and downstream processing, the molecular sequence of proinsulin folding is not completely understood. Proinsulin requires proline isomerization for correct folding. Since FK506-binding protein 2 (FKBP2) is an ER-resident proline isomerase, we hypothesized that FKBP2 contributes to proinsulin folding. We found that FKBP2 co-immunoprecipitated with proinsulin and its chaperone GRP94 and that inhibition of FKBP2 expression increased proinsulin turnover with reduced intracellular proinsulin and insulin levels. This phenotype was accompanied by an increased proinsulin secretion and the formation of proinsulin high-molecular-weight complexes, a sign of proinsulin misfolding. FKBP2 knockout in pancreatic β-cells increased apoptosis without detectable up-regulation of ER stress response genes. Interestingly, FKBP2 mRNA was overexpressed in β-cells from pancreatic islets of T2D patients. Based on molecular modeling and an in vitro enzymatic assay, we suggest that proline at position 28 of the proinsulin B-chain (P28) is the substrate of FKBP2's isomerization activity. We propose that this isomerization step catalyzed by FKBP2 is an essential sequence required for correct proinsulin folding.
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Abstract
![]()
Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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Laganowsky A, Clemmer DE, Russell DH. Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions. Annu Rev Biophys 2021; 51:63-77. [PMID: 34932911 PMCID: PMC9086101 DOI: 10.1146/annurev-biophys-102221-101121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structures and conformational dynamics of proteins, protein complexes, and their noncovalent interactions with other molecules are controlled specifically by the Gibbs free energy (entropy and enthalpy) of the system. For some organisms, temperature is highly regulated, but the majority of biophysical studies are carried out at room, nonphysiological temperature. In this review, we describe variable-temperature electrospray ionization (vT-ESI) mass spectrometry (MS)-based studies with unparalleled sensitivity, dynamic range, and selectivity for studies of both cold- and heat-induced chemical processes. Such studies provide direct determinations of stabilities, reactivities, and thermodynamic measurements for native and non-native structures of proteins and protein complexes and for protein-ligand interactions. Highlighted in this review are vT-ESI-MS studies that reveal 40 different conformers of chymotrypsin inhibitor 2, a classic two-state (native → unfolded) unfolder, and thermochemistry for a model membrane protein system binding lipid and its regulatory protein. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas, USA; ,
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas, USA; ,
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Raab SA, El-Baba TJ, Laganowsky A, Russell DH, Valentine SJ, Clemmer DE. Protons Are Fast and Smart; Proteins Are Slow and Dumb: On the Relationship of Electrospray Ionization Charge States and Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1553-1561. [PMID: 34151568 PMCID: PMC9003666 DOI: 10.1021/jasms.1c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present simple considerations of how differences in time scales of motions of protons, the lightest and fastest chemical moiety, and the much longer time scales associated with the dynamics of proteins, among the heaviest and slowest analytes, may allow many protein conformations from solution to be kinetically trapped during the process of electrospraying protein solutions into the gas phase. In solution, the quantum nature of protons leads them to change locations by tunneling, an instantaneous process; moreover, the Grotthuss mechanism suggests that these small particles can respond nearly instantaneously to the dynamic motions of proteins that occur on much longer time scales. A conformational change is accompanied by favorable or unfavorable variations in the free energy of the system, providing the impetus for solvent ↔ protein proton exchange. Thus, as thermal distributions of protein conformations interconvert, protonation states rapidly respond, as specific acidic and basic sites are exposed or protected. In the vacuum of the mass spectrometer, protons become immobilized in locations that are specific to the protein conformations from which they were incorporated. In this way, conformational states from solution are preserved upon electrospraying them into the gas phase. These ideas are consistent with the exquisite sensitivity of electrospray mass spectra to small changes of the local environment that alter protein structure in solution. We might remember this approximation for the protonation of proteins in solution with the colloquial expression-protons are fast and smart; proteins are slow and dumb.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Stephen J Valentine
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Sivaraman T, Richa T. Cryptic intermediates and metastable states of proteins as predicted by OneG computational method. J Biomol Struct Dyn 2021; 40:7899-7914. [PMID: 33764262 DOI: 10.1080/07391102.2021.1904288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Understanding structural excursions of proteins under folding conditions is crucial to map energy landscapes of proteins. In the present study, OneG computational tool has been used for analyzing possible existence of cryptic intermediates and metastable states of 26 proteins for which three prerequisite inputs of the OneG such as atomic coordinates of proteins, free energy of unfolding (ΔGU) and free energy of exchange (ΔGHX) determined in the absence of denaturant were available during the course of the study. The veraciousness of the tool on predicting the partially folded states of the proteins has been comprehensively described using experimental data available for 15 of the 26 proteins. Meanwhile, possible existence of partially structured states in the folding pathways of 11 other proteins has also been delineated as predicted by the OneG. In addition to mapping the folding pathways of proteins, the salient merits of the tool on systematically addressing the discrepancy between the ΔGU and the ΔGHX of the proteins have also been dealt.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thirunavukkarasu Sivaraman
- Drug Design and Discovery Lab, Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore, Tamil Nadu, India
| | - Tambi Richa
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
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Wang S, Liu Z, Yang M, Zhou Y, Yang M, Long M, Fang F, Guo J. The differences in characteristics of extracellular polymeric substances of flocs and anammox granules impacted aggregation. Bioprocess Biosyst Eng 2021; 44:1711-1720. [PMID: 33768321 DOI: 10.1007/s00449-021-02554-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
Extracellular polymeric substances (EPS) are considered crucial components in the formation of microbial aggregates such as biofilms, flocs and granules. However, the role of EPS in sludge aggregation is still unclear. In this study, the differences in EPS characteristics of anammox granular sludge (AG), anammox floc sludge (AF) and activated floc sludge (AS) were investigated to clarify its role in granular aggregation. The results showed that the flocculation ability of EPS extracted from AG (62.8 ± 2.3%) was notably higher than that of EPS extracted from AF (35.7 ± 1.7%) and AS (17.3 ± 1.5%). The zeta potential and hydrophobicity of EPS showed the same tendency. In addition, the PN/PS ratio of AG, AF and AS were 7.66, 4.62 and 3.93, respectively. FTIR, XPS and 3D-EEM fluorescence spectra results revealed that anammox granular sludge has a higher ratio of hydrophobic groups, α-helixs/(β-sheets and random coils), intermolecular hydrogen bonds, and aromatic amino acids, and a lower ratio of electronegative groups. Anammox granular sludge exhibited high aggregation ability, because its EPS had higher zeta potential, hydrophobicity and intermolecular hydrogen bond ratio. This work provides a better understanding of the high aggregation ability of anammox granules and a theoretical basis for improving granules proportion and retention ability of microbes in reactor system.
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Affiliation(s)
- Shuai Wang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Zihan Liu
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Mingming Yang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.,Yangtze Ecology and Environment Co., Ltd, Wuhan, 430062, China
| | - Yang Zhou
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Mansu Yang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Man Long
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Fang Fang
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
| | - Jinsong Guo
- College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
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10
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Shimizu S, Takada M, Wada K, Ikake H, Muroga Y. Conformational transition of Poly-L-proline studied by IR, NMR, and SAXS. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Bojarska J, Remko M, Breza M, Madura I, Fruziński A, Wolf WM. A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI. Pharmaceuticals (Basel) 2020; 13:E338. [PMID: 33114370 PMCID: PMC7692516 DOI: 10.3390/ph13110338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022] Open
Abstract
Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO-), -N+ and -COOH(-COO-), -NH and -COOH(-COO-), -NH+ and -COOH(-COO-), and -NH2+ and -COOH(-COO-). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Milan Remko
- Remedika, Luzna 9, 85104 Bratislava, Slovakia;
| | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia;
| | - Izabela Madura
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Andrzej Fruziński
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
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12
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Downhill, Ultrafast and Fast Folding Proteins Revised. Int J Mol Sci 2020; 21:ijms21207632. [PMID: 33076540 PMCID: PMC7589632 DOI: 10.3390/ijms21207632] [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: 08/30/2020] [Revised: 10/06/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023] Open
Abstract
Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form.
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Sever AIM, Konermann L. Gas Phase Protein Folding Triggered by Proton Stripping Generates Inside-Out Structures: A Molecular Dynamics Simulation Study. J Phys Chem B 2020; 124:3667-3677. [DOI: 10.1021/acs.jpcb.0c01934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander I. M. Sever
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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14
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Sreenivasan S, Narayan M. Learnings from Protein Folding Projected onto Amyloid Misfolding. ACS Chem Neurosci 2019; 10:3911-3913. [PMID: 31456389 DOI: 10.1021/acschemneuro.9b00445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The 1990s saw a revolution in our understanding of the protein folding pathways of both disulfide-bond-containing proteins and purely conformational folders. High-resolution maps of the folding trajectories, made possible by innovative experimental design, revealed the presence of multiple intermediates, their formation and consumption, and the network of interactions between them that lead to the formation of the folded protein from its unfolded state. The same level of detail has heretofore remained elusive as far as the amyloid aggregation pathways of prion-like proteins are concerned. Nevertheless, a recent development that led to the resolution of intermediates in amyloidogenic trajectories, without resort to their separation, is likely to not only advance our basic understanding of the atomic- and molecular-level interactions guiding amyloid misfolding but also impact interventional efforts in their associated pathologies.
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Affiliation(s)
- Sreeprasad Sreenivasan
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas 79968, United States
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15
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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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16
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Fuller DR, Conant CR, El-Baba TJ, Zhang Z, Molloy KR, Zhang CS, Hales DA, Clemmer DE. Monitoring the stabilities of a mixture of peptides by mass-spectrometry-based techniques. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:73-81. [PMID: 30773926 PMCID: PMC7702224 DOI: 10.1177/1469066718798718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Biomolecular degradation plays a key role in proteostasis. Typically, proteolytic enzymes degrade proteins into smaller peptides by breaking amino acid bonds between specific residues. Cleavage around proline residues is often missed and requires highly specific enzymes for peptide processing due to the cyclic proline side-chain. However, degradation can occur spontaneously (i.e. in the absence of enzymes). In this study, the influence of the first residue on the stability of a series of penultimate proline containing peptides, with the sequence Xaa-Pro-Gly-Gly (where Xaa is any amino acid), is investigated with mass spectrometry techniques. Peptides were incubated as mixtures at various solution temperatures (70℃ to 90℃) and were periodically sampled over the duration of the experiment. At elevated temperatures, we observe dissociation after the Xaa-Pro motif for all sequences, but at different rates. Transition state thermochemistry was obtained by studying the temperature-dependent kinetics and although all peptides show relatively small differences in the transition state free energies (∼95 kJ/mol), there is significant variability in the transition state entropy and enthalpy. This demonstrates that the side-chain of the first amino acid has a significant influence on the stability of the Xaa-Pro sequence. From these data, we demonstrate the ability to simultaneously measure the dissociation kinetics and relative transition state thermochemistries for a mixture of peptides, which vary only in the identity of the N-terminal amino acid.
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Affiliation(s)
- Daniel R Fuller
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | | | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Zhichao Zhang
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | | | - Connie S Zhang
- Department of Chemistry, Hendrix College, Conway, AR, USA
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, AR, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, USA
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17
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Huang KY, Horng JC. Impacts of the Terminal Charged Residues on Polyproline Conformation. J Phys Chem B 2018; 123:138-147. [DOI: 10.1021/acs.jpcb.8b10864] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Arai M. Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins. Biophys Rev 2018; 10:163-181. [PMID: 29307002 PMCID: PMC5899706 DOI: 10.1007/s12551-017-0346-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022] Open
Abstract
Extensive experimental and theoretical studies have advanced our understanding of the mechanisms of folding and binding of globular proteins, and coupled folding and binding of intrinsically disordered proteins (IDPs). The forces responsible for conformational changes and binding are common in both proteins; however, these mechanisms have been separately discussed. Here, we attempt to integrate the mechanisms of coupled folding and binding of IDPs, folding of small and multi-subdomain proteins, folding of multimeric proteins, and ligand binding of globular proteins in terms of conformational selection and induced-fit mechanisms as well as the nucleation–condensation mechanism that is intermediate between them. Accumulating evidence has shown that both the rate of conformational change and apparent rate of binding between interacting elements can determine reaction mechanisms. Coupled folding and binding of IDPs occurs mainly by induced-fit because of the slow folding in the free form, while ligand binding of globular proteins occurs mainly by conformational selection because of rapid conformational change. Protein folding can be regarded as the binding of intramolecular segments accompanied by secondary structure formation. Multi-subdomain proteins fold mainly by the induced-fit (hydrophobic collapse) mechanism, as the connection of interacting segments enhances the binding (compaction) rate. Fewer hydrophobic residues in small proteins reduce the intramolecular binding rate, resulting in the nucleation–condensation mechanism. Thus, the folding and binding of globular proteins and IDPs obey the same general principle, suggesting that the coarse-grained, statistical mechanical model of protein folding is promising for a unified theoretical description of all mechanisms.
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Affiliation(s)
- Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
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19
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Feller G. Protein folding at extreme temperatures: Current issues. Semin Cell Dev Biol 2017; 84:129-137. [PMID: 28941878 DOI: 10.1016/j.semcdb.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 08/18/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
The range of temperatures compatible with life is currently estimated from -25°C, as exemplified by metabolically active bacteria between sea ice crystals, and up to 122°C in hydrothermal vents as exemplified by the archaeon Methanopyrus kandleri. In the context of protein folding, as soon as a polypeptide emerges from the ribosome, it is exposed to the effects of environmental temperatures. Recent investigations have shown that the rate of protein folding is not adapted to extreme temperatures and should be very fast at high temperature and low in cold environments. This lack of adaptation is driven by kinetic constraints on protein stability. To counteract the deleterious effects of fast protein folding in hyperthermophiles, chaperones such as the Trigger Factor hold and slow down the rate of folding intermediates. Prolyl isomerization, a rate-limiting step in the folding of many proteins, is strongly temperature-dependent and impairs folding of psychrophilic proteins in the cold. This is compensated by reduction of the proline content in cold-adapted proteins, by an increased number of prolyl isomerases encoded in the genome of psychrophilic microorganisms and by overexpression of prolyl isomerases under low temperature cultivation. After folding, the native state is reached and although extremophilic proteins share the same fold, dramatic differences in stability have been recorded by differential scanning calorimetry.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, Institute of Chemistry B6a, 4000 Liège-Sart Tilman, Belgium.
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20
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Sevilhano T, de Carvalho RF, Oliveira NADJ, Oliveira JE, Maltarollo VG, Trossini G, Garcez R, Bartolini P. Molecular cloning and characterization of pirarucu (Arapaima gigas) follicle-stimulating hormone and luteinizing hormone β-subunit cDNAs. PLoS One 2017; 12:e0183545. [PMID: 28846736 PMCID: PMC5573580 DOI: 10.1371/journal.pone.0183545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/07/2017] [Indexed: 02/04/2023] Open
Abstract
The common gonadotrophic hormone α-subunit (GTHα) has been previously isolated by our research group from A. gigas pituitaries; in the present work the cDNA sequences encoding FSHβ and LHβ subunits have also been isolated from the same species of fish. The FSH β-subunit consists of 126 amino acids with a putative 18 amino acid signal peptide and a 108 amino acid mature peptide, while the LH β-subunit consists of 141 amino acids with a putative 24 amino acid amino acid signal peptide and a 117 amino acid mature peptide. The highest identity, based on the amino acid sequences, was found with the order of Anguilliformes (61%) for FSHβ and of Cypriniformes (76%) for LHβ, followed by Siluriformes, 53% for FSHβ and 75% for LHβ. Interestingly, the identity with the corresponding human amino acid sequences was still remarkable: 45.1% for FSHβ and 51.4% for LHβ. Three dimensional models of ag-FSH and ag-LH, generated by using the crystal structures of h-FSH and h-LH as the respective templates and carried out via comparative modeling and molecular dynamics simulations, suggested the presence of the so-called "seat-belt", favored by a disulfide bond formed between the 3rd and 12th cysteine in both β-subunits. The sequences found will be used for the biotechnological synthesis of A. gigas gonadotrophic hormones (ag-FSH and ag-LH). In a first approach, to ascertain that the cloned transcripts allow the expression of the heterodimeric hormones, ag-FSH has been synthesized in human embryonic kidney 293 (HEK293) cells, preliminarily purified and characterized.
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Affiliation(s)
- Thais Sevilhano
- Biotechnology Department, IPEN-CNEN/SP, Cidade Universitária, São Paulo, SP, Brazil
| | | | | | | | | | - Gustavo Trossini
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Riviane Garcez
- Genetic Ichthyology Laboratory, Bioscience Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Paolo Bartolini
- Biotechnology Department, IPEN-CNEN/SP, Cidade Universitária, São Paulo, SP, Brazil
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21
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El-Baba TJ, Woodall DW, Raab SA, Fuller DR, Laganowsky A, Russell DH, Clemmer DE. Melting Proteins: Evidence for Multiple Stable Structures upon Thermal Denaturation of Native Ubiquitin from Ion Mobility Spectrometry-Mass Spectrometry Measurements. J Am Chem Soc 2017; 139:6306-6309. [DOI: 10.1021/jacs.7b02774] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tarick J. El-Baba
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W. Woodall
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Shannon A. Raab
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel R. Fuller
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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22
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Mishra J, Hande P, Sharma P, Bhardwaj A, Rajput R, Misra K. Characterization of nucleobases in sea buckthorn leaves: An HPTLC approach. J LIQ CHROMATOGR R T 2017. [DOI: 10.1080/10826076.2017.1283517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jigni Mishra
- Department of Biochemical Sciences, Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi
| | - Prashant Hande
- Anchrom Test Lab Pvt Ltd, Mulund East, Mumbai, Maharashtra
| | - Priyanka Sharma
- Department of Biochemical Sciences, Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi
| | - Anuja Bhardwaj
- Department of Biochemical Sciences, Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi
| | - Rakhee Rajput
- Department of Biochemical Sciences, Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi
| | - Kshipra Misra
- Department of Biochemical Sciences, Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi
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23
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Narayan A, Campos LA, Bhatia S, Fushman D, Naganathan AN. Graded Structural Polymorphism in a Bacterial Thermosensor Protein. J Am Chem Soc 2017; 139:792-802. [DOI: 10.1021/jacs.6b10608] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
| | - Luis A. Campos
- National Biotechnology Center, Consejo Superior
de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Sandhya Bhatia
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bangalore 560065, India
| | - David Fushman
- Department
of Chemistry and Biochemistry, Center for Biomolecular Structure and
Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
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24
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Robinson AC, Majumdar A, Schlessman JL, García-Moreno E B. Charges in Hydrophobic Environments: A Strategy for Identifying Alternative States in Proteins. Biochemistry 2016; 56:212-218. [DOI: 10.1021/acs.biochem.6b00843] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Jamie L. Schlessman
- Chemistry
Department, United States Naval Academy, 572M Holloway Rd MS 9B, Annapolis, Maryland 21402, United States
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25
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Properties of the Amide Bond Involving Proline 4,5-methanologues: an Experimental and Theoretical Study. Isr J Chem 2016. [DOI: 10.1002/ijch.201600106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Das S, Pal U, Chatterjee M, Pramanik SK, Banerji B, Maiti NC. Envisaging Structural Insight of a Terminally Protected Proline Dipeptide by Raman Spectroscopy and Density Functional Theory Analyses. J Phys Chem A 2016; 120:9829-9840. [PMID: 27973793 DOI: 10.1021/acs.jpca.6b10017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Supriya Das
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Uttam Pal
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Moumita Chatterjee
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sumit Kumar Pramanik
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Biswadip Banerji
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Nakul C. Maiti
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
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27
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Oh KI, Smith-Dupont KB, Markiewicz BN, Gai F. Kinetics of peptide folding in lipid membranes. Biopolymers 2016; 104:281-90. [PMID: 25808575 DOI: 10.1002/bip.22640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/12/2015] [Accepted: 02/14/2015] [Indexed: 12/31/2022]
Abstract
Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Kathryn B Smith-Dupont
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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28
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Shi L, Holliday AE, Bohrer BC, Kim D, Servage KA, Russell DH, Clemmer DE. "Wet" Versus "Dry" Folding of Polyproline. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1037-47. [PMID: 27059978 PMCID: PMC5152579 DOI: 10.1007/s13361-016-1372-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/20/2016] [Accepted: 02/22/2016] [Indexed: 05/06/2023]
Abstract
When the all-cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all-trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all-cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions-indicating that some transitions observed in water (i.e., "wet" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline. Graphical Abstract ᅟ.
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Affiliation(s)
- Liuqing Shi
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Alison E Holliday
- Department of Chemistry, Moravian College, Bethlehem, PA, 18018, USA
| | - Brian C Bohrer
- Department of Chemistry, University of Southern Indiana, Evansville, IN, 47712, USA
| | - Doyong Kim
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Kelly A Servage
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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29
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Englander SW, Mayne L, Kan ZY, Hu W. Protein Folding-How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry. Annu Rev Biophys 2016; 45:135-52. [PMID: 27145881 DOI: 10.1146/annurev-biophys-062215-011121] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments over time include the HX pulse labeling method with nuclear magnetic resonance analysis, the fragment separation method, the addition to it of mass spectrometric (MS) analysis, and recent improvements in the HX MS technique and data analysis. Also, the discovery of protein foldons and their role supplies an essential interpretive link. Recent work using HX pulse labeling with MS analysis finds that a number of proteins fold by stepping through a reproducible sequence of native-like intermediates in an ordered pathway. The stepwise nature of the pathway is dictated by the cooperative foldon unit construction of the protein. The pathway order is determined by a sequential stabilization principle; prior native-like structure guides the formation of adjacent native-like structure. This view does not match the funneled energy landscape paradigm of a very large number of folding tracks, which was framed before foldons were known and is more appropriate for the unguided residue-level search to surmount an initial kinetic barrier rather than for the overall unfolded-state to native-state folding pathway.
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Affiliation(s)
- S Walter Englander
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059; , , ,
| | - Leland Mayne
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059; , , ,
| | - Zhong-Yuan Kan
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059; , , ,
| | - Wenbing Hu
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059; , , ,
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30
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Seaiby C, Zabuga AV, Svendsen A, Rizzo TR. IR-induced conformational isomerization of a helical peptide in a cold ion trap. J Chem Phys 2016; 144:014304. [DOI: 10.1063/1.4939528] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Caroline Seaiby
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Annette Svendsen
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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31
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Abstract
Amyloid fibrils are associated with a number of human diseases. These aggregatively misfolded intermolecular β-sheet assemblies constitute some of the most challenging targets in structural biology because to their complexity, size, and insolubility. Here, protocols and controls are described for experiments designed to study hydrogen-bonding in amyloid fibrils indirectly, by transferring information about amide proton occupancy in the fibrils to the dimethyl sulfoxide-denatured state. Since the denatured state is amenable to solution NMR spectroscopy, the method can provide residue-level-resolution data on hydrogen exchange for the monomers that make up the fibrils.
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Affiliation(s)
- Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, BSP 209, 91 N. Eagleville Rd., Storrs, CT, 06269-3125, USA.
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32
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Berger G, Vilchis‐Reyes M, Hanessian S. Structural Properties and Stereochemically Distinct Folding Preferences of 4,5‐
cis
and
trans
‐Methano‐
L
‐Proline Oligomers: The Shortest Crystalline PPII‐Type Helical Proline‐Derived Tetramer. Angew Chem Int Ed Engl 2015; 54:13268-72. [DOI: 10.1002/anie.201506208] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Gilles Berger
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
- Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Université Libre de Bruxelles, Campus Plaine CP205/5, Université Libre de Bruxelles, Bd du Triomphe, 1050 Brussels (Belgium)
| | - Miguel Vilchis‐Reyes
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
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33
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Berger G, Vilchis‐Reyes M, Hanessian S. Structural Properties and Stereochemically Distinct Folding Preferences of 4,5‐
cis
and
trans
‐Methano‐
L
‐Proline Oligomers: The Shortest Crystalline PPII‐Type Helical Proline‐Derived Tetramer. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gilles Berger
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
- Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Université Libre de Bruxelles, Campus Plaine CP205/5, Université Libre de Bruxelles, Bd du Triomphe, 1050 Brussels (Belgium)
| | - Miguel Vilchis‐Reyes
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
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34
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Shi L, Holliday AE, Khanal N, Russell DH, Clemmer DE. Configurationally-Coupled Protonation of Polyproline-7. J Am Chem Soc 2015; 137:8680-3. [DOI: 10.1021/jacs.5b04287] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Liuqing Shi
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alison E. Holliday
- Department
of Chemistry, Moravian College, Bethlehem, Pennsylvania 18018, United States
| | - Neelam Khanal
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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35
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The Mechanism and Function of Group II Chaperonins. J Mol Biol 2015; 427:2919-30. [PMID: 25936650 DOI: 10.1016/j.jmb.2015.04.013] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022]
Abstract
Protein folding in the cell requires the assistance of enzymes collectively called chaperones. Among these, the chaperonins are 1-MDa ring-shaped oligomeric complexes that bind unfolded polypeptides and promote their folding within an isolated chamber in an ATP-dependent manner. Group II chaperonins, found in archaea and eukaryotes, contain a built-in lid that opens and closes over the central chamber. In eukaryotes, the chaperonin TRiC/CCT is hetero-oligomeric, consisting of two stacked rings of eight paralogous subunits each. TRiC facilitates folding of approximately 10% of the eukaryotic proteome, including many cytoskeletal components and cell cycle regulators. Folding of many cellular substrates of TRiC cannot be assisted by any other chaperone. A complete structural and mechanistic understanding of this highly conserved and essential chaperonin remains elusive. However, recent work is beginning to shed light on key aspects of chaperonin function and how their unique properties underlie their contribution to maintaining cellular proteostasis.
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36
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Abstract
How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼ 20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the "new view" model for protein folding. Emergent macroscopic foldon-foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the "how" and the "why" questions. The protein folding pathway depends on the same foldon units and foldon-foldon interactions that construct the native structure.
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Shi L, Holliday AE, Shi H, Zhu F, Ewing MA, Russell DH, Clemmer DE. Characterizing Intermediates Along the Transition from Polyproline I to Polyproline II Using Ion Mobility Spectrometry-Mass Spectrometry. J Am Chem Soc 2014; 136:12702-11. [DOI: 10.1021/ja505899g] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Liuqing Shi
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alison E. Holliday
- Department
of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Huilin Shi
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Feifei Zhu
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Michael A. Ewing
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Herrmann JM, Riemer J. Three approaches to one problem: protein folding in the periplasm, the endoplasmic reticulum, and the intermembrane space. Antioxid Redox Signal 2014; 21:438-56. [PMID: 24483706 DOI: 10.1089/ars.2014.5841] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE The bacterial periplasm, the endoplasmic reticulum (ER), and the intermembrane space (IMS) of mitochondria contain dedicated machineries for the incorporation of disulfide bonds into polypeptides, which cooperate with chaperones, proteases, and assembly factors during protein biogenesis. RECENT ADVANCES The mitochondrial disulfide relay was identified only very recently. The current knowledge of the protein folding machinery of the IMS will be described in detail in this review and compared with the "more established" systems of the periplasm and the ER. CRITICAL ISSUES While the disulfide relays of all three compartments adhere to the same principle, the specific designs and functions of these systems differ considerably. In particular, the cooperation with other folding systems makes the situation in each compartment unique. FUTURE DIRECTIONS The biochemical properties of the oxidation machineries are relatively well understood. However, it still remains largely unclear as to how the quality control systems of "oxidizing" compartments orchestrate the activities of oxidoreductases, chaperones, proteases, and signaling molecules to ensure protein homeostasis.
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Affiliation(s)
- Johannes M Herrmann
- 1 Department of Cell Biology, University of Kaiserslautern , Kaiserslautern, Germany
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39
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Feige MJ, Buchner J. Principles and engineering of antibody folding and assembly. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2024-2031. [PMID: 24931831 DOI: 10.1016/j.bbapap.2014.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 11/20/2022]
Abstract
Antibodies are uniquely suited to serve essential roles in the human immune defense as they combine several specific functions in one hetero-oligomeric protein. Their constant regions activate effector functions and their variable domains provide a stable framework that allows incorporation of highly diverse loop sequences. The combination of non-germline DNA recombination and mutation together with heavy and light chain assembly allows developing variable regions that specifically recognize essentially any antigen they may encounter. However, this diversity also requires tailor-made mechanisms to guarantee that folding and association of antibodies is carefully this diversity also requires tailor-made mechanisms to guarantee that folding and association of antibodies is carefully controlled before the protein is secreted from a plasma cell. Accordingly, the generic immunoglobulin fold β-barrel structure of antibody domains has been fine-tuned during evolution to fit the different requirements. Work over the past decades has identified important aspects of the folding and assembly of antibody domains and chains revealing domain specific variations of a general scheme. The most striking is the folding of an intrinsically disordered antibody domain in the context of its partner domain as the basis for antibody assembly and its control on the molecular level in the cell. These insights have not only allowed a better understanding of the antibody folding process but also provide a wealth of opportunities for rational optimization of antibody molecules. In this review, we summarize current concepts of antibody folding and assembly and discuss how they can be utilized to engineer antibodies with improved performance for different applications. This article is part of a Special Issue entitled: Recent advances in the molecular engineering of antibodies.
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Affiliation(s)
- Matthias J Feige
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis 38105, TN, USA.
| | - Johannes Buchner
- CIPSM at the Department of Chemistry, Technische Universität München, 85748 Garching, Germany.
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40
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Narayan A, Naganathan AN. Evidence for the sequential folding mechanism in RNase H from an ensemble-based model. J Phys Chem B 2014; 118:5050-8. [PMID: 24762044 DOI: 10.1021/jp500934f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of distinct protein folding pathways starting from an unfolded ensemble, and hence, the folding mechanism is an intricate function of protein size, sequence complexity, and stability conditions. This has traditionally been a contentious issue particularly because of the ensemble nature of conventional experiments that can mask the complexity of the underlying folding landscape. Recent hydrogen-exchange experiments combined with mass spectrometry (HX-MS) reveal that the folding of RNase H proceeds in a hierarchical fashion with distinct intermediates and following a single discrete path. In our current work, we provide computational evidence for this unique folding mechanism by employing a structure-based statistical mechanical model. Upon calibrating the energetic terms of the model with equilibrium measurements, we predict multiple intermediate states in the folding of RNase H that closely resemble experimental observations. Remarkably, a simplified landscape representation adequately captures the folding complexity and predicts the possibility of a well-defined sequence of folding events. We supplement the statistical model study with both explicit solvent molecular simulations of the helical units and electrostatic calculations to provide structural and energetic insights into the early and late stages of RNase H folding that hint at the frustrated nature of its folding landscape.
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Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
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41
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Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
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42
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Santucci R, Sinibaldi F, Patriarca A, Santucci D, Fiorucci L. Misfolded proteins and neurodegeneration: role of non-native cytochrome c in cell death. Expert Rev Proteomics 2014; 7:507-17. [DOI: 10.1586/epr.10.50] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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43
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Richa T, Sivaraman T. OneG-Vali: a computational tool for detecting, estimating and validating cryptic intermediates of proteins under native conditions. RSC Adv 2014. [DOI: 10.1039/c4ra04642k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Unfolding pathway of T4 lysozyme under native conditions as predicted by the OneG-Vali has been illustrated. Also, structural contexts of various states (native (N), cryptic intermediates (CIs) and unfolded (U) conformations) of the protein and the population of three CIs are depicted.
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Affiliation(s)
- Tambi Richa
- Structural Biology Laboratory
- Department of Bioinformatics
- School of Chemical and Biotechnology
- SASTRA University
- , India
| | - Thirunavukkarasu Sivaraman
- Structural Biology Laboratory
- Department of Bioinformatics
- School of Chemical and Biotechnology
- SASTRA University
- , India
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44
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Gasymov OK, Abduragimov AR, Glasgow BJ. Effect of short- and long-range interactions on trp rotamer populations determined by site-directed tryptophan fluorescence of tear lipocalin. PLoS One 2013; 8:e78754. [PMID: 24205305 PMCID: PMC3810256 DOI: 10.1371/journal.pone.0078754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/20/2013] [Indexed: 11/25/2022] Open
Abstract
In the lipocalin family, the conserved interaction between the main α-helix and the β-strand H is an ideal model to study protein side chain dynamics. Site-directed tryptophan fluorescence (SDTF) has successfully elucidated tryptophan rotamers at positions along the main alpha helical segment of tear lipocalin (TL). The rotamers assigned by fluorescent lifetimes of Trp residues corroborate the restriction expected based on secondary structure. Steric conflict constrains Trp residues to two (t, g−) of three possible χ1 (t, g−, g+) canonical rotamers. In this study, investigation focused on the interplay between rotamers for a single amino acid position, Trp 130 on the α-helix and amino acids Val 113 and Leu 115 on the H strand, i.e. long range interactions. Trp130 was substituted for Phe by point mutation (F130W). Mutations at positions 113 and 115 with combinations of Gly, Ala, Phe residues alter the rotamer distribution of Trp130. Mutations, which do not distort local structure, retain two rotamers (two lifetimes) populated in varying proportions. Replacement of either long range partner with a small amino acid, V113A or L115A, eliminates the dominance of the t rotamer. However, a mutation that distorts local structure around Trp130 adds a third fluorescence lifetime component. The results indicate that the energetics of long-range interactions with Trp 130 further tune rotamer populations. Diminished interactions, evident in W130G113A115, result in about a 22% increase of α-helix content. The data support a hierarchic model of protein folding. Initially the secondary structure is formed by short-range interactions. TL has non-native α-helix intermediates at this stage. Then, the long-range interactions produce the native fold, in which TL shows α-helix to β-sheet transitions. The SDTF method is a valuable tool to assess long-range interaction energies through rotamer distribution as well as the characterization of low-populated rotameric states of functionally important excited protein states.
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Affiliation(s)
- Oktay K. Gasymov
- Departments of Pathology and Laboratory Medicine and Ophthalmology and Jules Stein Eye Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (OG); (BG)
| | - Adil R. Abduragimov
- Departments of Pathology and Laboratory Medicine and Ophthalmology and Jules Stein Eye Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ben J. Glasgow
- Departments of Pathology and Laboratory Medicine and Ophthalmology and Jules Stein Eye Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (OG); (BG)
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45
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Walton TA, Rees DC. Structure and stability of the C-terminal helical bundle of the E. coli mechanosensitive channel of large conductance. Protein Sci 2013; 22:1592-601. [PMID: 24038743 DOI: 10.1002/pro.2360] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 12/19/2022]
Abstract
The crystal structure of the cytoplasmic domain (CTD) from the mechanosensitive channel of large conductance (MscL) in E. coli has been determined at 1.45 Å resolution. This domain forms a pentameric coiled coil similar to that observed in the structure of MscL from M. tuberculosis and also found in the cartilage oligomeric matrix protein (COMPcc). It contains canonical hydrophobic and atypical ionic interactions compared to previously characterized coiled coil structures. Thermodynamic analysis indicates that while the free EcMscL-CTD is less stable than other coiled coils, it is likely to remain folded in context of the full-length channel.
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Affiliation(s)
- Troy A Walton
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, 91125
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46
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Vahidi S, Stocks BB, Liaghati-Mobarhan Y, Konermann L. Submillisecond protein folding events monitored by rapid mixing and mass spectrometry-based oxidative labeling. Anal Chem 2013; 85:8618-25. [PMID: 23841479 DOI: 10.1021/ac401148z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Kinetic measurements can provide insights into protein folding mechanisms. However, the initial (submillisecond) stages of folding still represent a formidable analytical challenge. A number of ultrarapid triggering techniques have been available for some time, but coupling of these techniques with detection methods that are capable of providing detailed structural information has proven to be difficult. The current work addresses this issue by combining submillisecond mixing with laser-induced oxidative labeling. Apomyoglobin (aMb) serves as a model system for our measurements. Exposure of the protein to a brief pulse of hydroxyl radical (·OH) at different time points during folding introduces covalent modifications at solvent accessible side chains. The extent of labeling is monitored using mass spectrometry-based peptide mapping, providing spatially resolved measurements of changes in solvent accessibility. The submillisecond mixer used here improves the time resolution by a factor of 50 compared to earlier ·OH labeling experiments from our laboratory. Data obtained in this way indicate that early aMb folding events are driven by both local and sequence-remote docking of hydrophobic side chains. Assembly of a partially formed A(E)G(H) scaffold after 0.2 ms is followed by stepwise consolidation that ultimately yields the native state. Major conformational changes go to completion within 0.1 s. The technique introduced here is capable of providing in-depth structural information on very short time scales that have thus far been dominated by low resolution (global) spectroscopic probes. By employing submillisecond mixing in conjunction with slower mixing techniques, it is possible to observe complete folding pathways, from fractions of a millisecond all the way to minutes.
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Affiliation(s)
- Siavash Vahidi
- Departments of Chemistry and Biochemistry, The University of Western Ontario , London, Ontario, N6A 5B7, Canada
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47
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NMR as a tool to identify and characterize protein folding intermediates. Arch Biochem Biophys 2013; 531:90-9. [DOI: 10.1016/j.abb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/20/2022]
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48
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Morgan AA, Rubenstein E. Proline: the distribution, frequency, positioning, and common functional roles of proline and polyproline sequences in the human proteome. PLoS One 2013; 8:e53785. [PMID: 23372670 PMCID: PMC3556072 DOI: 10.1371/journal.pone.0053785] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 12/05/2012] [Indexed: 11/19/2022] Open
Abstract
Proline is an anomalous amino acid. Its nitrogen atom is covalently locked within a ring, thus it is the only proteinogenic amino acid with a constrained phi angle. Sequences of three consecutive prolines can fold into polyproline helices, structures that join alpha helices and beta pleats as architectural motifs in protein configuration. Triproline helices are participants in protein-protein signaling interactions. Longer spans of repeat prolines also occur, containing as many as 27 consecutive proline residues. Little is known about the frequency, positioning, and functional significance of these proline sequences. Therefore we have undertaken a systematic bioinformatics study of proline residues in proteins. We analyzed the distribution and frequency of 687,434 proline residues among 18,666 human proteins, identifying single residues, dimers, trimers, and longer repeats. Proline accounts for 6.3% of the 10,882,808 protein amino acids. Of all proline residues, 4.4% are in trimers or longer spans. We detected patterns that influence function based on proline location, spacing, and concentration. We propose a classification based on proline-rich, polyproline-rich, and proline-poor status. Whereas singlet proline residues are often found in proteins that display recurring architectural patterns, trimers or longer proline sequences tend be associated with the absence of repetitive structural motifs. Spans of 6 or more are associated with DNA/RNA processing, actin, and developmental processes. We also suggest a role for proline in Kruppel-type zinc finger protein control of DNA expression, and in the nucleation and translocation of actin by the formin complex.
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Affiliation(s)
- Alexander A. Morgan
- Department of Biochemistry and Genome Technology Center, Stanford University Medical School, Stanford, California, United States of America
| | - Edward Rubenstein
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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49
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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50
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Khanal A, Pan Y, Brown LS, Konermann L. Pulsed hydrogen/deuterium exchange mass spectrometry for time-resolved membrane protein folding studies. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1620-6. [PMID: 23280751 DOI: 10.1002/jms.3127] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/16/2012] [Accepted: 10/17/2012] [Indexed: 05/10/2023]
Abstract
Kinetic folding experiments by pulsed hydrogen/deuterium exchange (HDX) mass spectrometry (MS) are a well-established tool for water-soluble proteins. To the best of our knowledge, the current study is the first that applies this approach to an integral membrane protein. The native state of bacteriorhodopsin (BR) comprises seven transmembrane helices and a covalently bound retinal cofactor. BR exposure to sodium dodecyl sulfate (SDS) induces partial unfolding and retinal loss. We employ a custom-built three-stage mixing device for pulsed-HDX/MS investigations of BR refolding. The reaction is triggered by mixing SDS-denatured protein with bicelles. After a variable folding time (10 ms to 24 h), the protein is exposed to excess D(2) O buffer under rapid exchange conditions. The HDX pulse is terminated by acid quenching after 24 ms. Subsequent off-line analysis is performed by size exclusion chromatography and electrospray MS. These measurements yield the number of protected backbone N-H sites as a function of folding time, reflecting the recovery of secondary structure. Our results indicate that much of the BR secondary structure is formed quite late during the reaction, on a time scale of 10 s and beyond. It is hoped that in the future it will be possible to extend the pulsed-HDX/MS approach employed here to membrane proteins other than BR.
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Affiliation(s)
- Anil Khanal
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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