1
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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2
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Nam K, Arattu Thodika AR, Grundström C, Sauer UH, Wolf-Watz M. Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. J Chem Inf Model 2024; 64:150-163. [PMID: 38117131 PMCID: PMC10778088 DOI: 10.1021/acs.jcim.3c01618] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
This study explores ligand-driven conformational changes in adenylate kinase (AK), which is known for its open-to-close conformational transitions upon ligand binding and release. By utilizing string free energy simulations, we determine the free energy profiles for both enzyme opening and ligand release and compare them with profiles from the apoenzyme. Results reveal a three-step ligand release process, which initiates with the opening of the adenosine triphosphate-binding subdomain (ATP lid), followed by ligand release and concomitant opening of the adenosine monophosphate-binding subdomain (AMP lid). The ligands then transition to nonspecific positions before complete dissociation. In these processes, the first step is energetically driven by ATP lid opening, whereas the second step is driven by ATP release. In contrast, the AMP lid opening and its ligand release make minor contributions to the total free energy for enzyme opening. Regarding the ligand binding mechanism, our results suggest that AMP lid closure occurs via an induced-fit mechanism triggered by AMP binding, whereas ATP lid closure follows conformational selection. This difference in the closure mechanisms provides an explanation with implications for the debate on ligand-driven conformational changes of AK. Additionally, we determine an X-ray structure of an AK variant that exhibits significant rearrangements in the stacking of catalytic arginines, explaining its reduced catalytic activity. In the context of apoenzyme opening, the sequence of events is different. Here, the AMP lid opens first while the ATP lid remains closed, and the free energy associated with ATP lid opening varies with orientation, aligning with the reported AK opening and closing rate heterogeneity. Finally, this study, in conjunction with our previous research, provides a comprehensive view of the intricate interplay between various structural elements, ligands, and catalytic residues that collectively contribute to the robust catalytic power of the enzyme.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Abdul Raafik Arattu Thodika
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | | | - Uwe H. Sauer
- Department
of Chemistry, Umeå University, Umeå 90187, SE, Sweden
| | - Magnus Wolf-Watz
- Department
of Chemistry, Umeå University, Umeå 90187, SE, Sweden
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3
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Ma X, Albertsma J, Gabriels D, Horst R, Polat S, Snoeks C, Kapteijn F, Eral HB, Vermaas DA, Mei B, de Beer S, van der Veen MA. Carbon monoxide separation: past, present and future. Chem Soc Rev 2023; 52:3741-3777. [PMID: 37083229 PMCID: PMC10243283 DOI: 10.1039/d3cs00147d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Indexed: 04/22/2023]
Abstract
Large amounts of carbon monoxide are produced by industrial processes such as biomass gasification and steel manufacturing. The CO present in vent streams is often burnt, this produces a large amount of CO2, e.g., oxidation of CO from metallurgic flue gasses is solely responsible for 2.7% of manmade CO2 emissions. The separation of N2 from CO due to their very similar physical properties is very challenging, meaning that numerous energy-intensive steps are required for CO separation, making the CO separation from many process streams uneconomical in spite of CO being a valuable building block in the production of major chemicals through C1 chemistry and the production of linear hydrocarbons by the Fischer-Tropsch process. The development of suitable processes for the separation of carbon monoxide has both industrial and environmental significance. Especially since CO is a main product of electrocatalytic CO2 reduction, an emerging sustainable technology to enable carbon neutrality. This technology also requires an energy-efficient separation process. Therefore, there is a great need to develop energy efficient CO separation processes adequate for these different process streams. As such the urgency of separating carbon monoxide is gaining greater recognition, with research in the field becoming more and more crucial. This review details the principles on which CO separation is based and provides an overview of currently commercialised CO separation processes and their limitations. Adsorption is identified as a technology with the potential for CO separation with high selectivity and energy efficiency. We review the research efforts, mainly seen in the last decades, in developing new materials for CO separation via ad/bsorption and membrane technology. We have geared our review to both traditional CO sources and emerging CO sources, including CO production from CO2 conversion. To that end, a variety of emerging processes as potential CO2-to-CO technologies are discussed and, specifically, the need for CO capture after electrochemical CO2 reduction is highlighted, which is still underexposed in the available literature. Altogether, we aim to highlight the knowledge gaps that could guide future research to improve CO separation performance for industrial implementation.
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Affiliation(s)
- Xiaozhou Ma
- Chemical Engineering Department, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Jelco Albertsma
- Chemical Engineering Department, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Dieke Gabriels
- Chemical Engineering Department, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Rens Horst
- Science and Technology Faculty, University Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Sevgi Polat
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
- Chemical Engineering Department, Marmara University, 34854 İstanbul, Turkey
| | - Casper Snoeks
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - Freek Kapteijn
- Chemical Engineering Department, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Hüseyin Burak Eral
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - David A Vermaas
- Chemical Engineering Department, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Bastian Mei
- Industrial Chemistry, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Sissi de Beer
- Science and Technology Faculty, University Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Monique Ann van der Veen
- Chemical Engineering Department, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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4
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Salehi SM, Pezzella M, Willard A, Meuwly M, Karplus M. Water dynamics around T 0 vs R 4 of hemoglobin from local hydrophobicity analysis. J Chem Phys 2023; 158:025101. [PMID: 36641390 DOI: 10.1063/5.0129990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The local hydration around tetrameric hemoglobin (Hb) in its T0 and R4 conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the α1β2 and α2β1 interfaces, responsible for the quaternary T → R transition, which is encoded in the Monod-Wyman-Changeux model, as well as comparison with earlier computations of the solvent accessible surface area, makes clear that the two quantities measure different aspects of hydration. Local hydrophobicity quantifies the presence and structure of water molecules at the interface, whereas "buried surface" reports on the available space for solvent. For simulations with Hb frozen in its T0 and R4 states, the correlation coefficient between LH and buried surface is 0.36 and 0.44, respectively, but it increases considerably if the 95% confidence interval is used. The LH with Hb frozen and flexible changes little for most residues at the interfaces but is significantly altered for a few select ones: Thr41α, Tyr42α, Tyr140α, Trp37β, Glu101β (for T0) and Thr38α, Tyr42α, Tyr140α (for R4). The number of water molecules at the interface is found to increase by ∼25% for T0 → R4, which is consistent with earlier measurements. Since hydration is found to be essential to protein function, it is clear that hydration also plays an essential role in allostery.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Marco Pezzella
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Adam Willard
- Department of Chemistry MIT, Cambridge, Massachusetts 02139, USA
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Martin Karplus
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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5
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Morea V, Angelucci F, Tame JRH, Di Cera E, Bellelli A. Structural Basis of Sequential and Concerted Cooperativity. Biomolecules 2022; 12:biom12111651. [PMID: 36359000 PMCID: PMC9687781 DOI: 10.3390/biom12111651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Allostery is a property of biological macromolecules featuring cooperative ligand binding and regulation of ligand affinity by effectors. The definition was introduced by Monod and Jacob in 1963, and formally developed as the "concerted model" by Monod, Wyman, and Changeux in 1965. Since its inception, this model of cooperativity was seen as distinct from and not reducible to the "sequential model" originally formulated by Pauling in 1935, which was developed further by Koshland, Nemethy, and Filmer in 1966. However, it is difficult to decide which model is more appropriate from equilibrium or kinetics measurements alone. In this paper, we examine several cooperative proteins whose functional behavior, whether sequential or concerted, is established, and offer a combined approach based on functional and structural analysis. We find that isologous, mostly helical interfaces are common in cooperative proteins regardless of their mechanism. On the other hand, the relative contribution of tertiary and quaternary structural changes, as well as the asymmetry in the liganded state, may help distinguish between the two mechanisms.
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Affiliation(s)
- Veronica Morea
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR) c/o Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesco Angelucci
- Department of Life, Health, and Environmental Sciences, University of L’Aquila, Piazzale Salvatore Tommasi 1, 67100 L’Aquila, Italy
| | - Jeremy R. H. Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Andrea Bellelli
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
- Correspondence:
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6
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Liang Z, Su H, Ren X, Lin X, He Z, Li X, Zheng Y. Analysis of Key Genes Responsible for Low Urea Production in Saccharomyces cerevisiae JH301. Front Microbiol 2022; 13:894661. [PMID: 35558109 PMCID: PMC9087593 DOI: 10.3389/fmicb.2022.894661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 03/31/2022] [Indexed: 01/23/2023] Open
Abstract
There is a potential safety risk with ethyl carbamate (EC) in Hongqu Huangjiu production; 90% of the EC in rice wine is produced by the reaction of the urea with the alcohol of Saccharomyces cerevisiae. In our previous experiments, we screened and obtained a S. cerevisiae strain JH301 that offered low urea production. However, the key genes responsible for low urea production of strain JH301 remain unclear. Here, the whole genome sequencing of S. cerevisiae strain JH301 was accomplished via a next-generation high-throughput sequencing and long-read sequencing technology. There are six main pathways related to the urea metabolism of strain JH301 based on KEGG pathway mapping. Three species-specific genes are related to the urea metabolism pathways and were found in comparative genome analysis between strains JH301 and S288c during Hongqu Huangjiu production for the first time. Finally, the ARG80 gene was found to be likely a key gene responsible for low urea production of S. cerevisiae strain JH301, as determined by PCR and qRT-PCR check analyses from DNA and RNA levers. In conclusion, the results are useful for a scientific understanding of the mechanism of low urea production by Saccharomyces cerevisiae during Hongqu Huangjiu fermentation. It also is important to control the urea and EC contents in Hongqu Huangjiu production.
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Affiliation(s)
- Zhangcheng Liang
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, China.,Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, China
| | - Hao Su
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, China.,Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, China
| | - Xiangyun Ren
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, China.,Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, China
| | - Xiaozi Lin
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, China.,Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, China
| | - Zhigang He
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, China.,Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, China
| | - Xiangyou Li
- Fujian Pinghuhong Biological Technology Co., Ltd., Fuzhou, China
| | - Yan Zheng
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, China.,Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, China
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7
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Domino effect in allosteric signaling of peptide binding. J Mol Biol 2022; 434:167661. [DOI: 10.1016/j.jmb.2022.167661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022]
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8
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Meuwly M, Karplus M. The functional role of the hemoglobin-water interface. Mol Aspects Med 2021; 84:101042. [PMID: 34756740 DOI: 10.1016/j.mam.2021.101042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from in vitro, in vivo, and computational experiments (molecular dynamics simulations) are summarized and put into perspective. One of the main findings from the computations is that the stability of the deoxy, ligand-free T-state (T0) can be stabilized relative to the deoxy R-state (R0) only in sufficiently large simulation boxes for the hydrophobic effect to manifest itself. This effect directly influences protein stability and is operative also under physiological conditions. Furthermore, molecular simulations provide a dynamical interpretation of the Perutz model for Hb function. Results from experiments using higher protein concentrations and realistic cellular environments are also discussed. One of the next great challenges for computational studies, which as we show is likely to be taken up in the near future, is to provide a molecular-level understanding of the dynamics of proteins in such crowded environments.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056, Basel, Switzerland; Department of Chemistry, Brown University, Providence RI, USA.
| | - Martin Karplus
- Department of Chemistry, Harvard University, USA; Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000, Strasbourg, France.
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9
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Dixit VA, Blumberger J, Vyas SK. Methemoglobin formation in mutant hemoglobin α chains: electron transfer parameters and rates. Biophys J 2021; 120:3807-3819. [PMID: 34265263 DOI: 10.1016/j.bpj.2021.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/06/2021] [Accepted: 07/07/2021] [Indexed: 11/26/2022] Open
Abstract
Hemoglobin-mediated transport of dioxygen (O2) critically depends on the stability of the reduced (Fe2+) form of the heme cofactors. Some protein mutations stabilize the oxidized (Fe3+) state (methemoglobin, Hb M), causing methemoglobinemia, and can be lethal above 30%. The majority of the analyses of factors influencing Hb oxidation are retrospective and give insights only for inner-sphere mutations of heme (His58, His87). Herein, we report the first all-atom molecular dynamics simulations on both redox states and calculations of the Marcus electron transfer (ET) parameters for the α chain Hb oxidation and reduction rates for Hb M. The Hb wild-type (WT) and most of the studied α chain variants maintain globin structure except the Hb M Iwate (H87Y). The mutants forming Hb M tend to have lower redox potentials and thus stabilize the oxidized (Fe3+) state (in particular, the Hb Miyagi variant with K61E mutation). Solvent reorganization (λsolv 73-96%) makes major contributions to reorganization free energy, whereas protein reorganization (λprot) accounts for 27-30% except for the Miyagi and J-Buda variants (λprot ∼4%). Analysis of heme-solvent H-bonding interactions among variants provide insights into the role of Lys61 residue in stabilizing the Fe2+ state. Semiclassical Marcus ET theory-based calculations predict experimental kET for the Cyt b5-Hb complex and provide insights into relative reduction rates for Hb M in Hb variants. Thus, our methodology provides a rationale for the effect of mutations on the structure, stability, and Hb oxidation reduction rates and has potential for identification of mutations that result in methemoglobinemia.
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Affiliation(s)
- Vaibhav A Dixit
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani (BITS-Pilani), Rajasthan, India.
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Shivam Kumar Vyas
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani (BITS-Pilani), Rajasthan, India
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10
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Choi M, Kim JG, Muniyappan S, Kim H, Kim TW, Lee Y, Lee SJ, Kim SO, Ihee H. Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics. Chem Sci 2021; 12:8207-8217. [PMID: 34194711 PMCID: PMC8208487 DOI: 10.1039/d1sc01207j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
A salt bridge, one of the representative structural factors established by non-covalent interactions, plays a crucial role in stabilizing the structure and regulating the protein function, but its role in dynamic processes has been elusive. Here, to scrutinize the structural and functional roles of the salt bridge in the process of performing the protein function, we investigated the effects of salt bridges on the allosteric structural transition of homodimeric hemoglobin (HbI) by applying time-resolved X-ray solution scattering (TRXSS) to the K30D mutant, in which the interfacial salt bridges of the wild type (WT) are abolished. The TRXSS data of K30D are consistent with the kinetic model that requires one monomer intermediate in addition to three structurally distinct dimer intermediates (I1, I2, and I3) observed in WT and other mutants. The kinetic and structural analyses show that K30D has an accelerated biphasic transition from I2 to I3 by more than nine times compared to WT and lacks significant structural changes in the transition from R-like I2 to T-like I3 observed in WT, unveiling that the loss of the salt bridges interrupts the R-T allosteric transition of HbI. Besides, the correlation between the bimolecular CO recombination rates in K30D, WT, and other mutants reveals that the bimolecular CO recombination is abnormally decelerated in K30D, indicating that the salt bridges also affect the cooperative ligand binding in HbI. These comparisons of the structural dynamics and kinetics of K30D and WT show that the interfacial salt bridges not only assist the physical connection of two subunits but also play a critical role in the global structural signal transduction of one subunit to the other subunit via a series of well-organized structural transitions.
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Affiliation(s)
- Minseo Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Jong Goo Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Srinivasan Muniyappan
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Hanui Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Tae Wu Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Seong Ok Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
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11
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Pezzella M, El Hage K, Niesen MJM, Shin S, Willard AP, Meuwly M, Karplus M. Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin. J Phys Chem B 2020; 124:6540-6554. [PMID: 32589026 DOI: 10.1021/acs.jpcb.0c04320] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin (Hb) and dimeric melittin. For the T0 to R0 transition in Hb, it is found that LH provides additional molecular-level insight into the Perutz mechanism, i.e., the breaking and formation of salt bridges at the α1/β2 and α2/β1 interface is accompanied by changes in LH. For Hb in cubic water boxes with 90 and 120 Å edge length it is observed that following a decrease in LH as a consequence of reduced water density or change of water orientation at the protein/water interface the α/β interfaces are destabilized; this is a hallmark of the Perutz stereochemical model for the T to R transition in Hb. The present work thus provides a dynamical view of the classical structural model relevant to the molecular foundations of Hb function. For dimeric melittin, earlier results by Cheng and Rossky [ Nature 1998, 392, 696-699] are confirmed and interpreted on the basis of LH from simulations in which the protein structure is frozen. For the flexible melittin dimer, the changes in the local hydration can be as much as 30% greater than for the rigid dimer, reflecting the fact that protein and water dynamics are coupled.
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Affiliation(s)
- Marco Pezzella
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.,SABNP, Université Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Michiel J M Niesen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Sucheol Shin
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Martin Karplus
- Department of Chemistry, Harvard University, Cambridge, Massachusetts, United States.,Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 67000 Strasbourg, France
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12
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Functional (un)cooperativity in elevator transport proteins. Biochem Soc Trans 2020; 48:1047-1055. [PMID: 32573703 DOI: 10.1042/bst20190970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/17/2022]
Abstract
The activity of enzymes is subject to regulation at multiple levels. Cooperativity, the interconnected behavior of active sites within a protein complex, directly affects protein activity. Cooperativity is a mode of regulation that requires neither extrinsic factors nor protein modifications. Instead, it allows enzymes themselves to modulate reaction rates. Cooperativity is an important regulatory mechanism in soluble proteins, but also examples of cooperative membrane proteins have been described. In this review, we summarize the current knowledge on interprotomer cooperativity in elevator-type proteins, a class of membrane transporters characterized by large rigid-body movements perpendicular to the membrane, and highlight well-studied examples and experimental approaches.
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13
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Shibayama N. Allosteric transitions in hemoglobin revisited. Biochim Biophys Acta Gen Subj 2020; 1864:129335. [DOI: 10.1016/j.bbagen.2019.03.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 12/19/2022]
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14
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More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function. Catalysts 2019. [DOI: 10.3390/catal9121024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
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15
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Chen WR, Chou CC, Wang CC. Phthalides serve as potent modulators to boost fetal hemoglobin induction therapy for β-hemoglobinopathies. Blood Adv 2019; 3:1493-1498. [PMID: 31072835 PMCID: PMC6517670 DOI: 10.1182/bloodadvances.2019031120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/19/2019] [Indexed: 01/22/2023] Open
Abstract
Fetal hemoglobin (HbF) induction therapy has become the most promising strategy for treating β-hemoglobinopathies, including sickle-cell diseases and β-thalassemia. However, subtle but critical structural difference exists between HbF and normal adult hemoglobin (HbA), which inevitably leads to reduced binding of the endogenous modulator 2,3-bisphosphoglycerate (2,3-BPG) to HbF and thus increased oxygen affinity and decreased oxygen transport efficiency of HbF. We combined the oxygen equilibrium experiments, resonance Raman (RR) spectroscopy, and molecular docking modeling, and we discuss 2 phthalides, z-butylidenephthalide and z-ligustilide, that can effectively lower the oxygen affinity of HbF. They adjust it to a level closer to that of HbA and make it a more satisfactory oxygen carrier for adults. From the oxygen equilibrium curve measurements, we show that the 2 phthalides are more effective than 2,3-BPG for modulating HbF. The RR spectra show that phthalides allosterically stabilize the oxygenated HbF in the low oxygen affinity conformation, and the molecular docking modeling reveals that the 2 chosen phthalides interact with HbF via the cleft around the γ1/γ2 interface with a binding strength ∼1.6 times stronger than that of 2,3-BPG. We discuss the implications of z-butylidenephthalide and z-ligustilide in boosting the efficacy of HbF induction therapy to mitigate the clinical severities of β-hemoglobinopathies.
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Affiliation(s)
- Wei-Ren Chen
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan, Republic of China
| | - Chia-Cheng Chou
- National Center for High-performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan, Republic of China; and
| | - Chia C Wang
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan, Republic of China
- Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, Republic of China
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16
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Song K, Zhang J, Lu S. Progress in Allosteric Database. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:65-87. [PMID: 31707700 DOI: 10.1007/978-981-13-8719-7_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An allosteric mechanism refers to the biological regulation process wherein macromolecules propagate the effect of ligand binding at one site to a spatially distant orthosteric locus, thus affecting activity. The theory has remained a trending topic in biology research for over 50 years, since the understanding of allostery is fundamental for gleaning numerous biological processes and developing new drug therapies. In the past two decades, the allosteric paradigm has evolved into more descriptive models, with ever-expanding amounts of experimental data pertaining to newly identified allosteric molecules. The AlloSteric Database (ASD, accessible at http://mdl.shsmu.edu.cn/ASD ), which is a comprehensive knowledge repository, has provided the public with integrated information encompassing allosteric proteins, modulators, sites, pathways, and networks to investigate allostery since 2009. In this chapter, we introduce the history and usage of the ASD and give attention to specific applications that have benefited from the ASD.
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Affiliation(s)
- Kun Song
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
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17
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Lee YM, Liou YC. Gears-In-Motion: The Interplay of WW and PPIase Domains in Pin1. Front Oncol 2018; 8:469. [PMID: 30460195 PMCID: PMC6232885 DOI: 10.3389/fonc.2018.00469] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/04/2018] [Indexed: 01/22/2023] Open
Abstract
Pin1 belongs to the family of the peptidyl-prolyl cis-trans isomerase (PPIase), which is a class of enzymes that catalyze the cis/trans isomerization of the Proline residue. Pin1 is unique and only catalyzes the phosphorylated Serine/Threonine-Proline (S/T-P) motifs of a subset of proteins. Since the discovery of Pin1 as a key protein in cell cycle regulation, it has been implicated in numerous diseases, ranging from cancer to neurodegenerative diseases. The main features of Pin1 lies in its two main domains: the WW (two conserved tryptophan) domain and the PPIase domain. Despite extensive studies trying to understand the mechanisms of Pin1 functions, how these two domains contribute to the biological roles of Pin1 in cellular signaling requires more investigations. The WW domain of Pin1 is known to have a higher affinity to its substrate than that of the PPIase domain. Yet, the WW domain seems to prefer the trans configuration of phosphorylated S/T-P motif, while the PPIase catalyzes the cis to trans isomerasion. Such contradicting information has generated much confusion as to the actual mechanism of Pin1 function. In addition, dynamic allostery has been suggested to be important for Pin1 function. Henceforth, in this review, we will be looking at the progress made in understanding the function of Pin1, and how these understandings can aid us in overcoming the diseases implicated by Pin1 such as cancer during drug development.
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Affiliation(s)
- Yew Mun Lee
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
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18
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Nguyen MK, Jaillet L, Redon S. Generating conformational transition paths with low potential-energy barriers for proteins. J Comput Aided Mol Des 2018; 32:853-867. [PMID: 30069648 DOI: 10.1007/s10822-018-0137-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.
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Affiliation(s)
- Minh Khoa Nguyen
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
| | - Léonard Jaillet
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France.
| | - Stéphane Redon
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
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19
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Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
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Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
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20
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Chang S, Mizuno M, Ishikawa H, Mizutani Y. Tertiary dynamics of human adult hemoglobin fixed in R and T quaternary structures. Phys Chem Chem Phys 2018; 20:3363-3372. [PMID: 29260810 DOI: 10.1039/c7cp06287g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein dynamics of human adult hemoglobin and its mutants restricted in R and T quaternary states following ligand photolysis were studied by time-resolved resonance Raman spectroscopy. In the time-resolved spectra, we observed spectral changes of in-plane stretching modes of heme and the iron-histidine stretching mode of the Fe-His bond for all the hemoglobin samples. The βD99N mutant, which adopts the R state in both the ligand-bound and the deoxy forms, showed similar temporal behaviors in time-resolved resonance Raman spectra as wild-type recombinant hemoglobin until 10 μs, consistent with the fact that the mutant undergoes only the tertiary structural changes in the R state. The βN102T mutant, which adopts the T state in both the ligand-bound and the deoxy forms, showed much slower tertiary structural changes, suggesting that the EF helical motion is decelerated by the change of the intersubunit interactions. The present data indicate that the allosteric kinetic response between the interhelical hydrogen bonds of the EF helices and the intersubunit hydrogen bonds is bidirectional. The implications of these results for understanding the allosteric pathway of Hb are discussed in detail.
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Affiliation(s)
- Shanyan Chang
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
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21
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Campitelli P, Guo J, Zhou HX, Ozkan SB. Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1. J Phys Chem B 2018; 122:5623-5629. [PMID: 29361231 DOI: 10.1021/acs.jpcb.7b11971] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery, which is regulation from distant sites, plays a major role in biology. While traditional allostery is described in terms of conformational change upon ligand binding as an underlying principle, it is possible to have allosteric regulations without significant conformational change through modulating the conformational dynamics by altering the local effective elastic modulus of the protein upon ligand binding. Pin1 utilizes this dynamic allostery to regulate its function. It is a modular protein containing a WW domain and a larger peptidyl prolyl isomerase domain (PPIase) that isomerizes phosphoserine/threonine-proline (pS/TP) motifs. The WW domain serves as a docking module, whereas catalysis solely takes place within the PPIase domain. Here, we analyze the change in the dynamic flexibility profile of the PPIase domain upon ligand binding to the WW domain. Substrate binding to the WW domain induces the formation of a new rigid hinge site around the interface of the two domains and loosens the flexibility of a rigid site existing in the Apo form around the catalytic site. This hinge-shift mechanism enhances the dynamic coupling of the catalytic positions with the PPIase domain, where the rest of the domain can cooperatively respond to the local conformational changes around the catalytic site, leading to an increase in catalytic efficiency.
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Affiliation(s)
- Paul Campitelli
- Department of Physics and Center for Biological Physics , Arizona State University , Tempe , Arizona 85287 , United States
| | - Jingjing Guo
- School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , China
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics , Arizona State University , Tempe , Arizona 85287 , United States
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22
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Jorge S, Bringas M, Petruk A, Arrar M, Marti M, Skaf M, Costa F, Capece L, Sonati M, Estrin D. Understanding the molecular basis of the high oxygen affinity variant human hemoglobin Coimbra. Arch Biochem Biophys 2018; 637:73-78. [DOI: 10.1016/j.abb.2017.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 11/27/2022]
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23
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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24
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Delarue M, Koehl P, Orland H. Ab initio sampling of transition paths by conditioned Langevin dynamics. J Chem Phys 2017; 147:152703. [PMID: 29055326 DOI: 10.1063/1.4985651] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We propose a novel stochastic method to generate Brownian paths conditioned to start at an initial point and end at a given final point during a fixed time tf under a given potential U(x). These paths are sampled with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a local stochastic partial differential equation. This equation cannot be solved in general but we present several approximations that are valid either in the low temperature regime or in the presence of barrier crossing. We show that this method warrants the generation of statistically independent transition paths. It is computationally very efficient. We illustrate the method first on two simple potentials, the two-dimensional Mueller potential and the Mexican hat potential, and then on the multi-dimensional problem of conformational transitions in proteins using the "Mixed Elastic Network Model" as a benchmark.
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Affiliation(s)
- Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, USA
| | - Henri Orland
- Institut de Physique Théorique, CEA, URA 2306 du CNRS, F-91191 Gif-sur-Yvette, France and Beijing Computational Science Research Center, Building 9, East Zone, ZPark II, No.10 East Xibeiwang Road, Haidian District, Beijing 100193, China
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25
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Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations. Sci Rep 2017; 7:10926. [PMID: 28883619 PMCID: PMC5589765 DOI: 10.1038/s41598-017-11259-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Abstract
Human hemoglobin (Hb) is a benchmark protein of structural biology that shaped our view of allosterism over 60 years ago, with the introduction of the MWC model based on Perutz structures of the oxy(R) and deoxy(T) states and the more recent Tertiary Two-State model that proposed the existence of individual subunit states -“r” and “t”-, whose structure is yet unknown. Cooperative oxygen binding is essential for Hb function, and despite decades of research there are still open questions related to how tertiary and quaternary changes regulate oxygen affinity. In the present work, we have determined the free energy profiles of oxygen migration and for HisE7 gate opening, with QM/MM calculations of the oxygen binding energy in order to address the influence of tertiary differences in the control of oxygen affinity. Our results show that in the α subunit the low to high affinity transition is achieved by a proximal effect that mostly affects oxygen dissociation and is the driving force of the allosteric transition, while in the β subunit the affinity change results from a complex interplay of proximal and distal effects, including an increase in the HE7 gate opening, that as shown by free energy profiles promotes oxygen uptake.
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26
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Chen WR, Yu Y, Zulfajri M, Lin PC, Wang CC. Phthalide Derivatives from Angelica Sinensis Decrease Hemoglobin Oxygen Affinity: A New Allosteric-Modulating Mechanism and Potential Use as 2,3-BPG Functional Substitutes. Sci Rep 2017; 7:5504. [PMID: 28710372 PMCID: PMC5511246 DOI: 10.1038/s41598-017-04554-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
Angelica sinensis (AS), one of the most versatile herbal medicines remains widely used due to its multi-faceted pharmacologic activities. Besides its traditional use as the blood-nourishing tonic, its anti-hypertensive, anti-cardiovascular, neuroprotective and anti-cancer effects have been reported. Albeit the significant therapeutic effects, how AS exerts such diverse efficacies from the molecular level remains elusive. Here we investigate the influences of AS and four representative phthalide derivatives from AS on the structure and function of hemoglobin (Hb). From the spectroscopy and oxygen equilibrium experiments, we show that AS and the chosen phthalides inhibited the oxygenated Hb from transforming into the high-affinity “relaxed” (R) state, decreasing Hb’s oxygen affinity. It reveals that phthalides cooperate with the endogenous Hb modulator, 2,3-bisphosphoglycerate (2,3-BPG) to synergetically regulate Hb allostery. From the docking modeling, phthalides appear to interact with Hb mainly through its α1/α2 interface, likely strengthening four (out of six) Hb “tense” (T) state stabilizing salt-bridges. A new allosteric-modulating mechanism is proposed to rationalize the capacity of phthalides to facilitate Hb oxygen transport, which may be inherently correlated with the therapeutic activities of AS. The potential of phthalides to serve as 2,3-BPG substitutes/supplements and their implications in the systemic biology and preventive medicine are discussed.
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Affiliation(s)
- Wei-Ren Chen
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424, Republic of China
| | - Youqing Yu
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424, Republic of China
| | - Muhammad Zulfajri
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424, Republic of China
| | - Ping-Cheng Lin
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424, Republic of China
| | - Chia C Wang
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424, Republic of China. .,Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424, Republic of China.
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27
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Inoguchi N, Mizuno N, Baba S, Kumasaka T, Natarajan C, Storz JF, Moriyama H. Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice. PLoS One 2017; 12:e0174921. [PMID: 28362841 PMCID: PMC5376325 DOI: 10.1371/journal.pone.0174921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/17/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant. RESULTS Highland hemoglobin yielded at least two crystal types, in which the longest axes were 507 and 230 Å. Using the smaller unit cell crystal, the structure was solved at 2.2 Å resolution. The asymmetric unit contained two tetrameric hemoglobin molecules. CONCLUSIONS The analyses revealed that αPro50 in the highland hemoglobin variant promoted a stable interaction between αHis45 and heme that was not seen in the αHis50 lowland variant. The αPro50 mutation also altered the nature of atomic contacts at the α1β2/α2β1 intersubunit interfaces. These results demonstrate how affinity-altering changes in intersubunit interactions can be produced by mutations at structurally remote sites.
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Affiliation(s)
- Noriko Inoguchi
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Nobuhiro Mizuno
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Chandrasekhar Natarajan
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
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28
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Das A, Rui H, Nakamoto R, Roux B. Conformational Transitions and Alternating-Access Mechanism in the Sarcoplasmic Reticulum Calcium Pump. J Mol Biol 2017; 429:647-666. [PMID: 28093226 PMCID: PMC5467534 DOI: 10.1016/j.jmb.2017.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/31/2016] [Accepted: 01/08/2017] [Indexed: 11/22/2022]
Abstract
Ion pumps are integral membrane proteins responsible for transporting ions against concentration gradients across biological membranes. Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA), a member of the P-type ATPases family, transports two calcium ions per hydrolyzed ATP molecule via an "alternating-access" mechanism. High-resolution crystallographic structures provide invaluable insight on the structural mechanism of the ion pumping process. However, to understand the molecular details of how ATP hydrolysis is coupled to calcium transport, it is necessary to gain knowledge about the conformational transition pathways connecting the crystallographically resolved conformations. Large-scale transitions in SERCA occur at time-scales beyond the current reach of unbiased molecular dynamics simulations. Here, we overcome this challenge by employing the string method, which represents a transition pathway as a chainofstates linking two conformational endpoints. Using a multiscale methodology, we have determined all-atom transition pathways for three main conformational transitions responsible for the alternating-access mechanism. The present pathways provide a clear chronology and ordering of the key events underlying the active transport of calcium ions by SERCA. Important conclusions are that the conformational transition that leads to occlusion with bound ATP and calcium is highly concerted and cooperative, the phosphorylation of Asp351 causes areorganization of the cytoplasmic domains that subsequently drives the opening of the luminal gate, and thereclosing of luminal gate induces a shift in the cytoplasmic domains that subsequently enables the dephosphorylation of Asp351-P. Formation of transient residue-residue contacts along the conformational transitions predicted by the computations provide an experimental route to test the general validity of the computational pathways.
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Affiliation(s)
- Avisek Das
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago,IL 60637, USA
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago,IL 60637, USA
| | - Robert Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, PO Box 800886, 480Ray C. Hunt Drive, Charlottesville, VA 22908, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago,IL 60637, USA.
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Esquerra RM, Bibi BM, Tipgunlakant P, Birukou I, Soman J, Olson JS, Kliger DS, Goldbeck RA. Role of Heme Pocket Water in Allosteric Regulation of Ligand Reactivity in Human Hemoglobin. Biochemistry 2016; 55:4005-17. [PMID: 27355904 PMCID: PMC4978812 DOI: 10.1021/acs.biochem.6b00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water molecules can enter the heme pockets of unliganded myoglobins and hemoglobins, hydrogen bond with the distal histidine, and introduce steric barriers to ligand binding. The spectrokinetics of photodissociated CO complexes of human hemoglobin and its isolated α and β chains were analyzed for the effect of heme hydration on ligand rebinding. A strong coupling was observed between heme hydration and quaternary state. This coupling may contribute significantly to the 20-60-fold difference between the R- and T-state bimolecular CO binding rate constants and thus to the modulation of ligand reactivity that is the hallmark of hemoglobin allostery. Heme hydration proceeded over the course of several kinetic phases in the tetramer, including the R to T quaternary transition. An initial 150 ns hydration phase increased the R-state distal pocket water occupancy, nw(R), to a level similar to that of the isolated α (∼60%) and β (∼10%) chains, resulting in a modest barrier to ligand binding. A subsequent phase, concurrent with the first step of the R → T transition, further increased the level of heme hydration, increasing the barrier. The final phase, concurrent with the final step of the allosteric transition, brought the water occupancy of the T-state tetramer, nw(T), even higher and close to full occupancy in both the α and β subunits (∼90%). This hydration level could present an even larger barrier to ligand binding and contribute significantly to the lower iron reactivity of the T state toward CO.
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Affiliation(s)
- Raymond M. Esquerra
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Bushra M. Bibi
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Pooncharas Tipgunlakant
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Ivan Birukou
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - Jayashree Soman
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - John S. Olson
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - David S. Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Robert A. Goldbeck
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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Perkett MR, Mirijanian DT, Hagan MF. The allosteric switching mechanism in bacteriophage MS2. J Chem Phys 2016; 145:035101. [PMID: 27448905 PMCID: PMC4947040 DOI: 10.1063/1.4955187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/07/2016] [Indexed: 01/16/2023] Open
Abstract
We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.
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Affiliation(s)
- Matthew R Perkett
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| | - Dina T Mirijanian
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
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31
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Soloviov M, Das AK, Meuwly M. Strukturelle Interpretation metastabiler Zustände in Myoglobin-NO. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maksym Soloviov
- Departement für Chemie; Universität Basel; Klingelbergstraße 80 4056 Basel Schweiz
| | - Akshaya K. Das
- Departement für Chemie; Universität Basel; Klingelbergstraße 80 4056 Basel Schweiz
| | - Markus Meuwly
- Departement für Chemie; Universität Basel; Klingelbergstraße 80 4056 Basel Schweiz
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Soloviov M, Das AK, Meuwly M. Structural Interpretation of Metastable States in Myoglobin-NO. Angew Chem Int Ed Engl 2016; 55:10126-30. [DOI: 10.1002/anie.201604552] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Maksym Soloviov
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
| | - Akshaya K. Das
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
| | - Markus Meuwly
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
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33
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Ramírez CL, Petruk A, Bringas M, Estrin DA, Roitberg AE, Marti MA, Capece L. Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions. J Chem Theory Comput 2016; 12:3390-7. [DOI: 10.1021/acs.jctc.6b00278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Claudia L. Ramírez
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
- Dto.
de Química Biologica Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Ariel Petruk
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Mauro Bringas
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Dario A. Estrin
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Adrian E. Roitberg
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Marcelo A. Marti
- Dto.
de Química Biologica Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Luciana Capece
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
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Yang C, Choi J, Ihee H. The time scale of the quaternary structural changes in hemoglobin revealed using the transient grating technique. Phys Chem Chem Phys 2015; 17:22571-5. [PMID: 26272458 DOI: 10.1039/c5cp03059e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quaternary structural transition between the R and T states of human hemoglobin was investigated using the transient grating technique. The results presented herein reveal that the quaternary structural change accompanied by the R-T transition occurs within a few microseconds.
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Affiliation(s)
- Cheolhee Yang
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea.
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36
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Xiong L, Liu Z. Molecular dynamics study on folding and allostery in RfaH. Proteins 2015; 83:1582-92. [DOI: 10.1002/prot.24839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/18/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Liqin Xiong
- Department of Physics; Beijing Normal University; Beijing 100875 China
| | - Zhenxing Liu
- Department of Physics; Beijing Normal University; Beijing 100875 China
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37
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Ronda L, Bruno S, Bettati S, Storici P, Mozzarelli A. From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci 2015; 2:12. [PMID: 25988179 PMCID: PMC4428442 DOI: 10.3389/fmolb.2015.00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 11/23/2022] Open
Abstract
The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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Affiliation(s)
- Luca Ronda
- Department of Neurosciences, University of Parma Parma, Italy
| | - Stefano Bruno
- Department of Pharmacy, University of Parma Parma, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy ; Institute of Biophysics, Consiglio Nazionale delle Ricerche Pisa, Italy
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38
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Guo J, Pang X, Zhou HX. Two pathways mediate interdomain allosteric regulation in pin1. Structure 2014; 23:237-247. [PMID: 25543254 DOI: 10.1016/j.str.2014.11.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/24/2014] [Accepted: 11/14/2014] [Indexed: 01/27/2023]
Abstract
Allostery is an essential means for regulating biomolecular functions and provides unique opportunities for drug design, yet our ability to elucidate allosteric mechanisms remains limited. Here, based on extensive molecular dynamics simulations, we present an atomistic picture of the pathways mediating the allosteric regulation of the PPIase domain of Pin1 by its WW domain. Two pathways jointly propagate the action of substrate-WW binding to produce closure and rigidification of three PPIase catalytic-site loops. One pathway preexists in the apo protein, but remains dormant until substrate-WW binding completes the second. The reduction in conformational entropy and preorganization of the catalytic-site loops observed here may explain why substrate-WW binding enhances ligand affinity and catalytic activity of the PPIase domain and suggest a combination drug therapy for Pin1-related diseases. Whereas the traditional view of allostery has emphasized conformational transition, our study identifies a distinct role of conformational dynamics in eliciting allostery.
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Affiliation(s)
- Jingjing Guo
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; Department of Chemistry, School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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39
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40
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Jones EM, Monza E, Balakrishnan G, Blouin GC, Mak PJ, Zhu Q, Kincaid JR, Guallar V, Spiro TG. Differential control of heme reactivity in alpha and beta subunits of hemoglobin: a combined Raman spectroscopic and computational study. J Am Chem Soc 2014; 136:10325-39. [PMID: 24991732 PMCID: PMC4353013 DOI: 10.1021/ja503328a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Indexed: 12/05/2022]
Abstract
The use of hybrid hemoglobin (Hb), with mesoheme substituted for protoheme, allows separate monitoring of the α or β hemes along the allosteric pathway. Using resonance Raman (rR) spectroscopy in silica gel, which greatly slows protein motions, we have observed that the Fe-histidine stretching frequency, νFeHis, which is a monitor of heme reactivity, evolves between frequencies characteristic of the R and T states, for both α or β chains, prior to the quaternary R-T and T-R shifts. Computation of νFeHis, using QM/MM and the conformational search program PELE, produced remarkable agreement with experiment. Analysis of the PELE structures showed that the νFeHis shifts resulted from heme distortion and, in the α chain, Fe-His bond tilting. These results support the tertiary two-state model of ligand binding (Henry et al., Biophys. Chem. 2002, 98, 149). Experimentally, the νFeHis evolution is faster for β than for α chains, and pump-probe rR spectroscopy in solution reveals an inflection in the νFeHis time course at 3 μs for β but not for α hemes, an interval previously shown to be the first step in the R-T transition. In the α chain νFeHis dropped sharply at 20 μs, the final step in the R-T transition. The time courses are fully consistent with recent computational mapping of the R-T transition via conjugate peak refinement by Karplus and co-workers (Fischer et al., Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 5608). The effector molecule IHP was found to lower νFeHis selectively for α chains within the R state, and a binding site in the α1α2 cleft is suggested.
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Affiliation(s)
- Eric M. Jones
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Emanuele Monza
- Joint
BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Gurusamy Balakrishnan
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - George C. Blouin
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Piotr J. Mak
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Qianhong Zhu
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - James R. Kincaid
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Victor Guallar
- Joint
BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas G. Spiro
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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41
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Perkett MR, Hagan MF. Using Markov state models to study self-assembly. J Chem Phys 2014; 140:214101. [PMID: 24907984 PMCID: PMC4048447 DOI: 10.1063/1.4878494] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/30/2014] [Indexed: 11/14/2022] Open
Abstract
Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to construct MSMs that is applicable to modeling a broad class of multi-molecular assembly reactions. Distinct structures formed during assembly are distinguished by their undirected graphs, which are defined by strong subunit interactions. Spatial inhomogeneities of free subunits are accounted for using a recently developed Gaussian-based signature. Simplifications to this state identification are also investigated. The feasibility of this approach is demonstrated on two different coarse-grained models for virus self-assembly. We find good agreement between the dynamics predicted by the MSMs and long, unbiased simulations, and that the MSMs can reduce overall simulation time by orders of magnitude.
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Affiliation(s)
- Matthew R Perkett
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
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42
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Abstract
Proteins are fascinating supramolecular structures, which are able to recognize ligands transforming binding information into chemical signals. They can transfer information across the cell, can catalyse complex chemical reactions, and are able to transform energy into work with much more efficiency than any human engine. The unique abilities of proteins are tightly coupled with their dynamic properties, which are coded in a complex way in the sequence and carefully refined by evolution. Despite its importance, our experimental knowledge of protein dynamics is still rather limited, and mostly derived from theoretical calculations. I will review here, in a systematic way, the current state-of-the-art theoretical approaches to the study of protein dynamics, emphasizing the most recent advances, examples of use and the expected lines of development in the near future.
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Affiliation(s)
- Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 8, Barcelona 08028, Spain.
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Abstract
The question of how allostery works was posed almost 50 years ago. Since then it has been the focus of much effort. This is for two reasons: first, the intellectual curiosity of basic science and the desire to understand fundamental phenomena, and second, its vast practical importance. Allostery is at play in all processes in the living cell, and increasingly in drug discovery. Many models have been successfully formulated, and are able to describe allostery even in the absence of a detailed structural mechanism. However, conceptual schemes designed to qualitatively explain allosteric mechanisms usually lack a quantitative mathematical model, and are unable to link its thermodynamic and structural foundations. This hampers insight into oncogenic mutations in cancer progression and biased agonists' actions. Here, we describe how allostery works from three different standpoints: thermodynamics, free energy landscape of population shift, and structure; all with exactly the same allosteric descriptors. This results in a unified view which not only clarifies the elusive allosteric mechanism but also provides structural grasp of agonist-mediated signaling pathways, and guides allosteric drug discovery. Of note, the unified view reasons that allosteric coupling (or communication) does not determine the allosteric efficacy; however, a communication channel is what makes potential binding sites allosteric.
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Affiliation(s)
- Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Center for Cancer Research, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Center for Cancer Research, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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Reaction trajectory revealed by a joint analysis of protein data bank. PLoS One 2013; 8:e77141. [PMID: 24244274 PMCID: PMC3823880 DOI: 10.1371/journal.pone.0077141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/29/2013] [Indexed: 11/19/2022] Open
Abstract
Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article), and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.
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45
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Changeux JP. 50 years of allosteric interactions: the twists and turns of the models. Nat Rev Mol Cell Biol 2013; 14:819-29. [DOI: 10.1038/nrm3695] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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46
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Vesper MD, de Groot BL. Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Comput Biol 2013; 9:e1003232. [PMID: 24068910 PMCID: PMC3777908 DOI: 10.1371/journal.pcbi.1003232] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 08/03/2013] [Indexed: 11/18/2022] Open
Abstract
Hemoglobin is the prototypic allosteric protein. Still, its molecular allosteric mechanism is not fully understood. To elucidate the mechanism of cooperativity on an atomistic level, we developed a novel computational technique to analyse the coupling of tertiary and quaternary motions. From Molecular Dynamics simulations showing spontaneous quaternary transitions, we separated the transition trajectories into two orthogonal sets of motions: one consisting of intra-chain motions only (referred to as tertiary-only) and one consisting of global inter-chain motions only (referred to as quaternary-only). The two underlying subspaces are orthogonal by construction and their direct sum is the space of full motions. Using Functional Mode Analysis, we were able to identify a collective coordinate within the tertiary-only subspace that is correlated to the most dominant motion within the quaternary-only motions, hence providing direct insight into the allosteric coupling mechanism between tertiary and quaternary conformation changes. This coupling-motion is substantially different from tertiary structure changes between the crystallographic structures of the T- and R-state. We found that hemoglobin's allosteric mechanism of communication between subunits is equally based on hydrogen bonds and steric interactions. In addition, we were able to affect the T-to-R transition rates by choosing different histidine protonation states, thereby providing a possible atomistic explanation for the Bohr effect.
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Affiliation(s)
- Martin D. Vesper
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L. de Groot
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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Abstract
Pentameric ligand-gated ion channels (pLGICs) play a central role in intercellular communication in the nervous system and are involved in fundamental processes such as attention, learning, and memory. They are oligomeric protein assemblies that convert a chemical signal into an ion flux through the postsynaptic membrane, but the molecular mechanism of gating ions has remained elusive. Here, we present atomistic molecular dynamics simulations of the prokaryotic channels from Gloeobacter violaceus (GLIC) and Erwinia chrysanthemi (ELIC), whose crystal structures are thought to represent the active and the resting states of pLGICs, respectively, and of the eukaryotic glutamate-gated chloride channel from Caenorhabditis elegans (GluCl), whose open-channel structure was determined complexed with the positive allosteric modulator ivermectin. Structural observables extracted from the trajectories of GLIC and ELIC are used as progress variables to analyze the time evolution of GluCl, which was simulated in the absence of ivermectin starting from the structure with bound ivermectin. The trajectory of GluCl with ivermectin removed shows a sequence of structural events that couple agonist unbinding from the extracellular domain to ion-pore closing in the transmembrane domain. Based on these results, we propose a structural mechanism for the allosteric communication leading to deactivation/activation of the GluCl channel. This model of gating emphasizes the coupling between the quaternary twisting and the opening/closing of the ion pore and is likely to apply to other members of the pLGIC family.
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48
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Weinkam P, Sali A. Mapping polymerization and allostery of hemoglobin S using point mutations. J Phys Chem B 2013; 117:13058-68. [PMID: 23957820 DOI: 10.1021/jp4025156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hemoglobin is a complex system that undergoes conformational changes in response to oxygen, allosteric effectors, mutations, and environmental changes. Here, we study allostery and polymerization of hemoglobin and its variants by application of two previously described methods: (i) AllosMod for simulating allostery dynamics given two allosterically related input structures and (ii) a machine-learning method for dynamics- and structure-based prediction of the mutation impact on allostery (Weinkam et al. J. Mol. Biol. 2013, 425, 647-661), now applicable to systems with multiple coupled binding sites, such as hemoglobin. First, we predict the relative stabilities of substates and microstates of hemoglobin, which are determined primarily by entropy within our model. Next, we predict the impact of 866 annotated mutations on hemoglobin's oxygen binding equilibrium. We then discuss a subset of 30 mutations that occur in the presence of the sickle cell mutation and whose effects on polymerization have been measured. Seven of these HbS mutations occur in three predicted druggable binding pockets that might be exploited to directly inhibit polymerization; one of these binding pockets is not apparent in the crystal structure, but only in structures generated by AllosMod. For the 30 mutations, we predict that mutation-induced conformational changes within a single tetramer tend not to significantly impact polymerization; instead, these mutations more likely impact polymerization by directly perturbing a polymerization interface. Finally, our analysis of allostery allows us to hypothesize why hemoglobin evolved to have multiple subunits and a persistent low frequency sickle cell mutation.
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Affiliation(s)
- Patrick Weinkam
- Department of Bioengineering and Therapeutic Sciences, ‡Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco , San Francisco, California 94158, United States
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Changeux JP. The concept of allosteric interaction and its consequences for the chemistry of the brain. J Biol Chem 2013; 288:26969-26986. [PMID: 23878193 DOI: 10.1074/jbc.x113.503375] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Throughout this Reflections article, I have tried to follow up on the genesis in the 1960s and subsequent evolution of the concept of allosteric interaction and to examine its consequences within the past decades, essentially in the field of the neuroscience. The main conclusion is that allosteric mechanisms built on similar structural principles operate in bacterial regulatory enzymes, gene repressors (and the related nuclear receptors), rhodopsin, G-protein-coupled receptors, neurotransmitter receptors, ion channels, and so on from prokaryotes up to the human brain yet with important features of their own. Thus, future research on these basic cybernetic sensors is expected to develop in two major directions: at the elementary level, toward the atomic structure and molecular dynamics of the conformational changes involved in signal recognition and transduction, but also at a higher level of organization, the contribution of allosteric mechanisms to the modulation of brain functions.
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Affiliation(s)
- Jean-Pierre Changeux
- Collège de France, 75005 Paris and the Institut Pasteur, 75724 Paris Cedex 15, France.
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Sowole MA, Konermann L. Comparative analysis of oxy-hemoglobin and aquomet-hemoglobin by hydrogen/deuterium exchange mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:997-1005. [PMID: 23666601 DOI: 10.1007/s13361-013-0647-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/12/2013] [Accepted: 04/14/2013] [Indexed: 06/02/2023]
Abstract
The function of hemoglobin (Hb) as oxygen transporter is mediated by reversible O2 binding to Fe(2+) heme in each of the α and β subunits. X-ray crystallography revealed different subunit arrangements in oxy-Hb and deoxy-Hb. The deoxy state is stabilized by additional contacts, causing a rigidification that results in strong protection against hydrogen/deuterium exchange (HDX). Aquomet-Hb is a dysfunctional degradation product with four water-bound Fe(3+) centers. Heme release from aquomet-Hb is relatively facile, triggering oxidative damage of membrane lipids. Aquomet-Hb crystallizes in virtually the same conformation as oxy-Hb. Hence, it is commonly implied that the solution-phase properties of aquomet-Hb should resemble those of the oxy state. This work compares the structural dynamics of oxy-Hb and aquomet-Hb by HDX mass spectrometry (MS). It is found that the aquomet state exhibits a solution-phase structure that is significantly more dynamic, as manifested by elevated HDX levels. These enhanced dynamics affect the aquomet α and β subunits in a different fashion. The latter undergoes global destabilization, whereas the former shows elevated HDX levels only in the heme binding region. It is proposed that these enhanced dynamics play a role in facilitating heme release from aquomet-Hb. Our findings should be of particular interest to the MS community because oxy-Hb and aquomet-Hb serve as widely used test analytes for probing the relationship between biomolecular structure in solution and in the gas phase. We are not aware of any prior comparative HDX/MS experiments on oxy-Hb and aquomet-Hb.
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Affiliation(s)
- Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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