1
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Salvador-Garcia D, Jin L, Hensley A, Gölcük M, Gallaud E, Chaaban S, Port F, Vagnoni A, Planelles-Herrero VJ, McClintock MA, Derivery E, Carter AP, Giet R, Gür M, Yildiz A, Bullock SL. A force-sensitive mutation reveals a non-canonical role for dynein in anaphase progression. J Cell Biol 2024; 223:e202310022. [PMID: 38949648 PMCID: PMC11215527 DOI: 10.1083/jcb.202310022] [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: 04/29/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024] Open
Abstract
The diverse roles of the dynein motor in shaping microtubule networks and cargo transport complicate in vivo analysis of its functions significantly. To address this issue, we have generated a series of missense mutations in Drosophila Dynein heavy chain. We show that mutations associated with human neurological disease cause a range of defects, including impaired cargo trafficking in neurons. We also describe a novel microtubule-binding domain mutation that specifically blocks the metaphase-anaphase transition during mitosis in the embryo. This effect is independent from dynein's canonical role in silencing the spindle assembly checkpoint. Optical trapping of purified dynein complexes reveals that this mutation only compromises motor performance under load, a finding rationalized by the results of all-atom molecular dynamics simulations. We propose that dynein has a novel function in anaphase progression that depends on it operating in a specific load regime. More broadly, our work illustrates how in vivo functions of motors can be dissected by manipulating their mechanical properties.
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Affiliation(s)
- David Salvador-Garcia
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Li Jin
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew Hensley
- Department of Physics, University of California, Berkeley, Berkeley, CA, USA
| | - Mert Gölcük
- School of Mechanical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Emmanuel Gallaud
- Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Sami Chaaban
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fillip Port
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alessio Vagnoni
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Mark A. McClintock
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Emmanuel Derivery
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew P. Carter
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Régis Giet
- Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Mert Gür
- School of Mechanical Engineering, Istanbul Technical University, Istanbul, Turkey
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ahmet Yildiz
- Department of Physics, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Simon L. Bullock
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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2
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Park S, Kim MA, Sohn YC. Characterization of myoinhibitory peptide signaling system and its implication in larval metamorphosis and spawning behavior in Pacific abalone. Gen Comp Endocrinol 2024; 353:114521. [PMID: 38621462 DOI: 10.1016/j.ygcen.2024.114521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/15/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Myoinhibitory peptides (MIPs) affect various physiological functions, including juvenile hormone signaling, muscle contraction, larval development, and reproduction in invertebrates. Although MIPs are ligands for MIP and/or sex peptide receptors (MIP/SPRs) in diverse arthropods and model organisms belonging to Lophotrochozoa, the MIP signaling system has not yet been fully investigated in mollusks. In this study, we identified the MIP signaling system in the Pacific abalone Haliotis discus hannai (Hdh). Similar to the invertebrate MIPs, a total of eight paracopies of MIPs (named Hdh-MIP1 to Hdh-MIP8), harboring a WX5-7Wamide motif, except for Hdh-MIP2, were found in the Hdh-MIP precursor. Furthermore, we characterized a functional Hdh-MIPR, which responded to the Hdh-MIPs, except for Hdh-MIP2, possibly linked with the PKC/Ca2+ and PKA/cAMP signaling pathways. Hdh-MIPs delayed larval metamorphosis but increased the spawning behavior. These results suggest that the Hdh-MIP signaling system provides insights into the unique function of MIP in invertebrates.
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Affiliation(s)
- Sungwoo Park
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Mi Ae Kim
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea.
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3
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Kellogg GE. Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins. Molecules 2024; 29:2838. [PMID: 38930903 PMCID: PMC11207109 DOI: 10.3390/molecules29122838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
A method is described to deconstruct the network of hydropathic interactions within and between a protein's sidechain and its environment into residue-based three-dimensional maps. These maps encode favorable and unfavorable hydrophobic and polar interactions, in terms of spatial positions for optimal interactions, relative interaction strength, as well as character. In addition, these maps are backbone angle-dependent. After map calculation and clustering, a finite number of unique residue sidechain interaction maps exist for each backbone conformation, with the number related to the residue's size and interaction complexity. Structures for soluble proteins (~749,000 residues) and membrane proteins (~387,000 residues) were analyzed, with the latter group being subdivided into three subsets related to the residue's position in the membrane protein: soluble domain, core-facing transmembrane domain, and lipid-facing transmembrane domain. This work suggests that maps representing residue types and their backbone conformation can be reassembled to optimize the medium-to-high resolution details of a protein structure. In particular, the information encoded in maps constructed from the lipid-facing transmembrane residues appears to paint a clear picture of the protein-lipid interactions that are difficult to obtain experimentally.
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Affiliation(s)
- Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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4
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Mom R, Réty S, Mocquet V, Auguin D. Deciphering Molecular Mechanisms Involved in the Modulation of Human Aquaporins' Water Permeability by Zinc Cations: A Molecular Dynamics Approach. Int J Mol Sci 2024; 25:2267. [PMID: 38396944 PMCID: PMC10888569 DOI: 10.3390/ijms25042267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Aquaporins (AQPs) constitute a wide family of water channels implicated in all kind of physiological processes. Zinc is the second most abundant trace element in the human body and a few studies have highlighted regulation of AQP0 and AQP4 by zinc. In the present work, we addressed the putative regulation of AQPs by zinc cations in silico through molecular dynamics simulations of human AQP0, AQP2, AQP4, and AQP5. Our results align with other scales of study and several in vitro techniques, hence strengthening the reliability of this regulation by zinc. We also described two distinct putative molecular mechanisms associated with the increase or decrease in AQPs' water permeability after zinc binding. In association with other studies, our work will help deciphering the interaction networks existing between zinc and channel proteins.
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Affiliation(s)
- Robin Mom
- Laboratoire de Biologie et Modélisation de la Cellule, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1293, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France; (S.R.); (V.M.)
- Research Group on Vestibular Pathophysiology, CNRS, Unit GDR2074, F-13331 Marseille, France
| | - Stéphane Réty
- Laboratoire de Biologie et Modélisation de la Cellule, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1293, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France; (S.R.); (V.M.)
| | - Vincent Mocquet
- Laboratoire de Biologie et Modélisation de la Cellule, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1293, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France; (S.R.); (V.M.)
| | - Daniel Auguin
- Laboratoire de Physiologie, Ecologie et Environnement (P2E), UPRES EA 1207/USC INRAE-1328, UFR Sciences et Techniques, Université d’Orléans, F-45067 Orléans, France
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5
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Tomar V, Rikkerink EHA, Song J, Sofkova-Bobcheva S, Bus VGM. Structure-Function Characterisation of Eop1 Effectors from the Erwinia-Pantoea Clade Reveals They May Acetylate Their Defence Target through a Catalytic Dyad. Int J Mol Sci 2023; 24:14664. [PMID: 37834112 PMCID: PMC10572645 DOI: 10.3390/ijms241914664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The YopJ group of acetylating effectors from phytopathogens of the genera Pseudomonas and Ralstonia have been widely studied to understand how they modify and suppress their host defence targets. In contrast, studies on a related group of effectors, the Eop1 group, lag far behind. Members of the Eop1 group are widely present in the Erwinia-Pantoea clade of Gram-negative bacteria, which contains phytopathogens, non-pathogens and potential biocontrol agents, implying that they may play an important role in agroecological or pathological adaptations. The lack of research in this group of YopJ effectors has left a significant knowledge gap in their functioning and role. For the first time, we perform a comparative analysis combining AlphaFold modelling, in planta transient expressions and targeted mutational analyses of the Eop1 group effectors from the Erwinia-Pantoea clade, to help elucidate their likely activity and mechanism(s). This integrated study revealed several new findings, including putative binding sites for inositol hexakisphosphate and acetyl coenzyme A and newly postulated target-binding domains, and raises questions about whether these effectors function through a catalytic triad mechanism. The results imply that some Eop1s may use a catalytic dyad acetylation mechanism that we found could be promoted by the electronegative environment around the active site.
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Affiliation(s)
- Vishant Tomar
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Erik H. A. Rikkerink
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
| | - Janghoon Song
- Pear Research Institute, National Institute of Horticultural & Herbal Science, Rural Development Administration, Naju 58216, Republic of Korea
| | - Svetla Sofkova-Bobcheva
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Vincent G. M. Bus
- Hawkes Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4130, New Zealand;
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Kellogg GE, Cen Y, Dukat M, Ellis KC, Guo Y, Li J, May AE, Safo MK, Zhang S, Zhang Y, Desai UR. Merging cultures and disciplines to create a drug discovery ecosystem at Virginia commonwealth university: Medicinal chemistry, structural biology, molecular and behavioral pharmacology and computational chemistry. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:255-269. [PMID: 36863508 PMCID: PMC10619687 DOI: 10.1016/j.slasd.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
The Department of Medicinal Chemistry, together with the Institute for Structural Biology, Drug Discovery and Development, at Virginia Commonwealth University (VCU) has evolved, organically with quite a bit of bootstrapping, into a unique drug discovery ecosystem in response to the environment and culture of the university and the wider research enterprise. Each faculty member that joined the department and/or institute added a layer of expertise, technology and most importantly, innovation, that fertilized numerous collaborations within the University and with outside partners. Despite moderate institutional support with respect to a typical drug discovery enterprise, the VCU drug discovery ecosystem has built and maintained an impressive array of facilities and instrumentation for drug synthesis, drug characterization, biomolecular structural analysis and biophysical analysis, and pharmacological studies. Altogether, this ecosystem has had major impacts on numerous therapeutic areas, such as neurology, psychiatry, drugs of abuse, cancer, sickle cell disease, coagulopathy, inflammation, aging disorders and others. Novel tools and strategies for drug discovery, design and development have been developed at VCU in the last five decades; e.g., fundamental rational structure-activity relationship (SAR)-based drug design, structure-based drug design, orthosteric and allosteric drug design, design of multi-functional agents towards polypharmacy outcomes, principles on designing glycosaminoglycans as drugs, and computational tools and algorithms for quantitative SAR (QSAR) and understanding the roles of water and the hydrophobic effect.
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Affiliation(s)
- Glen E Kellogg
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA.
| | - Yana Cen
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Malgorzata Dukat
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Keith C Ellis
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Jiong Li
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Aaron E May
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Martin K Safo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Shijun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA.
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7
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Salvador-Garcia D, Jin L, Hensley A, Gölcük M, Gallaud E, Chaaban S, Port F, Vagnoni A, Planelles-Herrero VJ, McClintock MA, Derivery E, Carter AP, Giet R, Gür M, Yildiz A, Bullock SL. A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551815. [PMID: 37577480 PMCID: PMC10418259 DOI: 10.1101/2023.08.03.551815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The cytoplasmic dynein-1 (dynein) motor organizes cells by shaping microtubule networks and moving a large variety of cargoes along them. However, dynein's diverse roles complicate in vivo studies of its functions significantly. To address this issue, we have used gene editing to generate a series of missense mutations in Drosophila Dynein heavy chain (Dhc). We find that mutations associated with human neurological disease cause a range of defects in larval and adult flies, including impaired cargo trafficking in neurons. We also describe a novel mutation in the microtubule-binding domain (MTBD) of Dhc that, remarkably, causes metaphase arrest of mitotic spindles in the embryo but does not impair other dynein-dependent processes. We demonstrate that the mitotic arrest is independent of dynein's well-established roles in silencing the spindle assembly checkpoint. In vitro reconstitution and optical trapping assays reveal that the mutation only impairs the performance of dynein under load. In silico all-atom molecular dynamics simulations show that this effect correlates with increased flexibility of the MTBD, as well as an altered orientation of the stalk domain, with respect to the microtubule. Collectively, our data point to a novel role of dynein in anaphase progression that depends on the motor operating in a specific load regime. More broadly, our work illustrates how cytoskeletal transport processes can be dissected in vivo by manipulating mechanical properties of motors.
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Affiliation(s)
| | - Li Jin
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andrew Hensley
- Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Mert Gölcük
- Department of Mechanical Engineering, Istanbul Technical University, Istanbul, 34437, Turkey
| | - Emmanuel Gallaud
- Institut de Génétique et Développement de Rennes - UMR 6290, Université de Rennes, F-35000 Rennes, France
| | - Sami Chaaban
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Fillip Port
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Current address: Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alessio Vagnoni
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Current address: Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9RX, UK
| | | | - Mark A. McClintock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Emmanuel Derivery
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andrew P. Carter
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Régis Giet
- Institut de Génétique et Développement de Rennes - UMR 6290, Université de Rennes, F-35000 Rennes, France
| | - Mert Gür
- Department of Mechanical Engineering, Istanbul Technical University, Istanbul, 34437, Turkey
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ahmet Yildiz
- Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Simon L. Bullock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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8
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Kellogg GE, Marabotti A, Spyrakis F, Mozzarelli A. HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham. Front Mol Biosci 2023; 10:1194962. [PMID: 37351551 PMCID: PMC10282649 DOI: 10.3389/fmolb.2023.1194962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
A long-lasting goal of computational biochemists, medicinal chemists, and structural biologists has been the development of tools capable of deciphering the molecule-molecule interaction code that produces a rich variety of complex biomolecular assemblies comprised of the many different simple and biological molecules of life: water, small metabolites, cofactors, substrates, proteins, DNAs, and RNAs. Software applications that can mimic the interactions amongst all of these species, taking account of the laws of thermodynamics, would help gain information for understanding qualitatively and quantitatively key determinants contributing to the energetics of the bimolecular recognition process. This, in turn, would allow the design of novel compounds that might bind at the intermolecular interface by either preventing or reinforcing the recognition. HINT, hydropathic interaction, was a model and software code developed from a deceptively simple idea of Donald Abraham with the close collaboration with Glen Kellogg at Virginia Commonwealth University. HINT is based on a function that scores atom-atom interaction using LogP, the partition coefficient of any molecule between two phases; here, the solvents are water that mimics the cytoplasm milieu and octanol that mimics the protein internal hydropathic environment. This review summarizes the results of the extensive and successful collaboration between Abraham and Kellogg at VCU and the group at the University of Parma for testing HINT in a variety of different biomolecular interactions, from proteins with ligands to proteins with DNA.
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Affiliation(s)
- Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Anna Marabotti
- Department of Chemistry and Biology “A Zambelli”, University of Salerno, Fisciano (SA), Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma and Institute of Biophysics, Parma, Italy
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9
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AL Mughram MH, Catalano C, Herrington NB, Safo MK, Kellogg GE. 3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins. Front Mol Biosci 2023; 10:1116868. [PMID: 37056722 PMCID: PMC10086146 DOI: 10.3389/fmolb.2023.1116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 03/30/2023] Open
Abstract
The aliphatic hydrophobic amino acid residues—alanine, isoleucine, leucine, proline and valine—are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary, and to a lesser extent, tertiary and quaternary structure. However, favorable hydrophobic interactions involving the sidechains of these residue types are generally less significant than the unfavorable set arising from interactions with polar atoms. Importantly, the constellation of interactions between residue sidechains and their environments can be recorded as three-dimensional maps that, in turn, can be clustered. The clustered average map sets compose a library of interaction profiles encoding interaction strengths, interaction types and the optimal 3D position for the interacting partners. This library is backbone angle-dependent and suggests solvent and lipid accessibility for each unique interaction profile. In this work, in addition to analysis of soluble proteins, a large set of membrane proteins that contained optimized artificial lipids were evaluated by parsing the structures into three distinct components: soluble extramembrane domain, lipid facing transmembrane domain, core transmembrane domain. The aliphatic residues were extracted from each of these sets and passed through our calculation protocol. Notable observations include: the roles of aliphatic residues in soluble proteins and in the membrane protein’s soluble domains are nearly identical, although the latter are slightly more solvent accessible; by comparing maps calculated with sidechain-lipid interactions to maps ignoring those interactions, the potential extent of residue-lipid and residue-interactions can be assessed and likely exploited in structure prediction and modeling; amongst these residue types, the levels of lipid engagement show isoleucine as the most engaged, while the other residues are largely interacting with neighboring helical residues.
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Affiliation(s)
- Mohammed H. AL Mughram
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Noah B. Herrington
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Martin K. Safo
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Glen E. Kellogg
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Glen E. Kellogg,
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10
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Patidar I, Palaka BK, Katike U, Velmurugan Ilavarasi A, Tulsi, Mohanty SS, Ampasala DR. Structural elucidation of ETHR-A and ETHR-B from Plutella xylostella and insight into non-conservative mutations in transmembrane helix-6. J Biomol Struct Dyn 2023; 41:12572-12585. [PMID: 36683288 DOI: 10.1080/07391102.2023.2167112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023]
Abstract
The development of Diamondback moth (DBM) depends on the ecdysis triggering hormone receptor (ETHR); a neuronal membrane G-protein coupled receptor (GPCR) connected to the metamorphosis cascade. Lepidopteran insect DBM is an infamous pest of cruciferous plants. This study examined the full-length coding sequences (CDS) of PxETHR-A and PxETHR-B from the DBM genome. The three-dimensional (3 D) models of both receptors were generated in an inactive state. The behaviour and stability of receptors were examined using molecular dynamics simulations in a lipid membrane system for 300 ns and established a GPCR family-based view. Secondary interactions within receptors were studied to know more about factors contributing to their stability. Multiple sequence alignment revealed conserved features of insect ETHRs those compared to the GPCR family proteins. These features were helpful during the evaluation of the molecular models of both receptors. Side-chain orientation of conserved residues, non-conserved and conserved hydrogen-bond networks (HBN) and hydrophobic clusters were examined in the structures of both receptors. The non-conserved residues L6.35, T6.39, C/S6.43, and L6.48, are present in a conserved position on the transmembrane helix-6 (TM6) of ETHRs. In TM6, PxETHR-A and PxETHR-B differ at positions C/S6.43 and Y/F6.51, both being part of the HBN.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ishwar Patidar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Bhagath Kumar Palaka
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Umamahesh Katike
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Tulsi
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Saswati Sarita Mohanty
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Dinakara Rao Ampasala
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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11
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AL Mughram MH, Herrington NB, Catalano C, Kellogg GE. Systematized analysis of secondary structure dependence of key structural features of residues in soluble and membrane-bound proteins. J Struct Biol X 2021; 5:100055. [PMID: 34934943 PMCID: PMC8654985 DOI: 10.1016/j.yjsbx.2021.100055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 11/27/2021] [Indexed: 11/27/2022] Open
Abstract
Knowledge of three-dimensional protein structure is integral to most modern drug discovery efforts. Recent advancements have highlighted new techniques for 3D protein structure determination and, where structural data cannot be collected experimentally, prediction of protein structure. We have undertaken a major effort to use existing protein structures to collect, characterize, and catalogue the inter-atomic interactions that define and compose 3D structure by mapping hydropathic interaction environments as maps in 3D space. This work has been performed on a residue-by-residue basis, where we have seen evidence for relationships between environment character, residue solvent-accessible surface areas and their secondary structures. In this graphical review, we apply principles from our earlier studies and expand the scope to all common amino acid residue types in both soluble and membrane proteins. Key to this analysis is parsing the Ramachandran plot to an 8-by-8 chessboard to define secondary structure bins. Our analysis yielded a number of quantitative discoveries: 1) increased fraction of hydrophobic residues (alanine, isoleucine, leucine, phenylalanine and valine) in membrane proteins compared to their fractions in soluble proteins; 2) less burial coupled with significant increases in favorable hydrophobic interactions for hydrophobic residues in membrane proteins compared to soluble proteins; and 3) higher burial and more favorable polar interactions for polar residues now preferring the interior of membrane proteins. These observations and the supporting data should provide benchmarks for current studies of protein residues in different environments and may be able to guide future protein structure prediction efforts.
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Affiliation(s)
- Mohammed H. AL Mughram
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Noah B. Herrington
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Claudio Catalano
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
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Herrington NB, Kellogg GE. 3D Interaction Homology: Computational Titration of Aspartic Acid, Glutamic Acid and Histidine Can Create pH-Tunable Hydropathic Environment Maps. Front Mol Biosci 2021; 8:773385. [PMID: 34805282 PMCID: PMC8595396 DOI: 10.3389/fmolb.2021.773385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/13/2021] [Indexed: 02/03/2023] Open
Abstract
Aspartic acid, glutamic acid and histidine are ionizable residues occupying various protein environments and perform many different functions in structures. Their roles are tied to their acid/base equilibria, solvent exposure, and backbone conformations. We propose that the number of unique environments for ASP, GLU and HIS is quite limited. We generated maps of these residue's environments using a hydropathic scoring function to record the type and magnitude of interactions for each residue in a 2703-protein structural dataset. These maps are backbone-dependent and suggest the existence of new structural motifs for each residue type. Additionally, we developed an algorithm for tuning these maps to any pH, a potentially useful element for protein design and structure building. Here, we elucidate the complex interplay between secondary structure, relative solvent accessibility, and residue ionization states: the degree of protonation for ionizable residues increases with solvent accessibility, which in turn is notably dependent on backbone structure.
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Affiliation(s)
- Noah B Herrington
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
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