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Bardeci NG, Tofolón E, Trajtenberg F, Caramelo J, Larrieux N, Rossi S, Buschiazzo A, Moreno S. The crystal structure of yeast regulatory subunit reveals key evolutionary insights into Protein Kinase A oligomerization. J Struct Biol 2021; 213:107732. [PMID: 33819633 DOI: 10.1016/j.jsb.2021.107732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 02/08/2023]
Abstract
Protein Kinase A (PKA) is a widespread enzyme that plays a key role in many signaling pathways from lower eukaryotes to metazoans. In mammals, the regulatory (R) subunits sequester and target the catalytic (C) subunits to proper subcellular locations. This targeting is accomplished by the dimerization and docking (D/D) domain of the R subunits. The activation of the holoenzyme depends on the binding of the second messenger cAMP. The only available structures of the D/D domain proceed from mammalian sources. Unlike dimeric mammalian counterparts, the R subunit from Saccharomyces cerevisiae (Bcy1) forms tetramers in solution. Here we describe the first high-resolution structure of a non-mammalian D/D domain. The tetramer in the crystals of the Bcy1 D/D domain is a dimer of dimers that retain the classical D/D domain fold. By using phylogenetic and structural analyses combined with site-directed mutagenesis, we found that fungal R subunits present an insertion of a single amino acid at the D/D domain that shifts the position of a downstream, conserved arginine. This residue participates in intra-dimer interactions in mammalian D/D domains, while due to this insertion it is involved in inter-dimer contacts in Bcy1, which are crucial for the stability of the tetramer. This surprising finding challenges well-established concepts regarding the oligomeric state within the PKAR protein family and provides important insights into the yet unexplored structural diversity of the D/D domains and the molecular determinants of R subunit oligomerization.
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Affiliation(s)
- Nicolás González Bardeci
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Buenos Aires C1428EHA, Argentina.
| | - Enzo Tofolón
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Buenos Aires C1428EHA, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Julio Caramelo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; Fundación Instituto Leloir, Instituto de investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires C1405BWE, Argentina
| | - Nicole Larrieux
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Silvia Rossi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Buenos Aires C1428EHA, Argentina
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Silvia Moreno
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Buenos Aires C1428EHA, Argentina.
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2
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Upadhyayula RS. Computational Investigation of Structural Interfaces of Protein Complexes with Short Linear Motifs. J Proteome Res 2020; 19:3254-3263. [DOI: 10.1021/acs.jproteome.0c00212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Raghavender Surya Upadhyayula
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, Rajasthan 302001, India
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3
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Nilofer C, Sukhwal A, Mohanapriya A, Sakharkar MK, Kangueane P. Small protein-protein interfaces rich in electrostatic are often linked to regulatory function. J Biomol Struct Dyn 2019; 38:3260-3279. [PMID: 31495333 DOI: 10.1080/07391102.2019.1657040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interaction (PPI) is critical for several biological functions in living cells through the formation of an interface. Therefore, it is of interest to characterize protein-protein interfaces using an updated non-redundant structural dataset of 2557 homo (identical subunits) and 393 hetero (different subunits) dimer protein complexes determined by X-ray crystallography. We analyzed the interfaces using van der Waals (vdW), hydrogen bonding and electrostatic energies. Results show that on average homo and hetero interfaces are similar. Hence, we further grouped the 2950 interfaces based on percentage vdW to total energies into dominant (≥60%) and sub-dominant (<60%) vdW interfaces. Majority (92%) of interfaces have dominant vdW energy with large interface size (146 ± 87 (homo) and 137 ± 76 (hetero) residues) and interface area (1622 ± 1135 Å2 (homo) and 1579 ± 1060 Å2 (hetero)). However, a proportion (8%) of interfaces have sub-dominant vdW energy with small interface size (85 ± 46 (homo) and 88 ± 36 (hetero) residues) and interface area (823 ± 538 Å2 (homo) and 881 ± 377 Å2 (hetero)). It is found that large interfaces have two-fold more interface area and interface size than small interfaces with increasing hydrogen bonding energy to interface size. However, small interfaces have three-fold more electrostatics energy than large interfaces with increasing electrostatics to interface size. Thus, 8% of complexes having small interfaces with limited interface area and sub-dominant vdW energy are rich in electrostatics. It is interesting to observe that complexes having small interfaces are often associated with regulatory function. Hence, the observed structural features with known molecular function provide insights for the better understanding of PPI.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Christina Nilofer
- Biomedical Informatics (P) Ltd., Pondicherry, India.,School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
| | - Anshul Sukhwal
- National Centre for Biological Sciences (NCBS), Bangalore, India
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4
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Tan X, Liu N, Yang M, Duan M, Zeng J. Design of peptide inhibitors of human papillomavirus 16 (HPV16) transcriptional regulator E1–E2 formation. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Here, we have proposed a new scheme of the computational combinatorial design approach to identify potential inhibitor peptides. It consists of four steps: (i) using “multiple copy simultaneous search” (MCSS) procedure to locate specific functional groups on the protein surface; (ii) the peptide main chain is constructed based on the location of favored N-methylacetamide (NMA) groups; (iii) molecular dynamics simulations of the complex formed between the constructed peptides with the target protein in explicit water molecules are carried to select the peptides with strong binding to the protein and (iv) the sequences of the stable peptides selected from (iii) are aligned and the frequencies of the amino acids at each position of peptide are calculated. Sequence patterns of potential inhibitors are determined based on the frequency of amino acids at each position. It was applied to design peptide inhibitors that bind to the E2 protein of HPV16 so as to disrupt its transcriptional regulator of E1–E2 complex formation. The sequence pattern of these potential inhibitors is in agreement with known inhibitors obtained from phage display, and the MCSS calculations indicate that a hydrophobic pocket on HPV16 E2 plays a significant role in E1–E2 formation and inhibitor-E2 binding.
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Affiliation(s)
- Xin Tan
- Department of Obstetrics and Gynaecology, West China Second University Hospital, No. 20, the Third Part Renmin South Road, Chengdu 610041, P. R. China
- Key Laboratory of Birth Defects and Related Diseases of Woman and Children, Sichuan University, Ministry of Education, No. 20, the Third Part Renmin South Road, Chengdu 610041, P. R. China
| | - Na Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Min Yang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P. R. China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jun Zeng
- School of Medical Sciences, Royal Melbourne Institute of Technology, Plenty Road, Bundoora, VIC 3083, Australia
- MedChemSoft Solutions, Level 3, 2 Brandon Park Drive, Wheelers Hill, VIC 3150, Australia
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5
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Kuroda D, Gray JJ. Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking. Bioinformatics 2016; 32:2451-6. [PMID: 27153634 DOI: 10.1093/bioinformatics/btw197] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 04/03/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATIONS Characterizing protein-protein interfaces and the hydrogen bonds is a first step to better understand proteins' structures and functions toward high-resolution protein design. However, there are few large-scale surveys of hydrogen bonds of interfaces. In addition, previous work of shape complementarity of protein complexes suggested that lower shape complementarity in antibody-antigen interfaces is related to their evolutionary origin. RESULTS Using 6637 non-redundant protein-protein interfaces, we revealed peculiar features of various protein complex types. In contrast to previous findings, the shape complementarity of antibody-antigen interfaces resembles that of the other interface types. These results highlight the importance of hydrogen bonds during evolution of protein interfaces and rectify the prevailing belief that antibodies have lower shape complementarity. CONTACT jgray@jhu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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6
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González Bardeci N, Caramelo JJ, Blumenthal DK, Rinaldi J, Rossi S, Moreno S. The PKA regulatory subunit from yeast forms a homotetramer: Low-resolution structure of the N-terminal oligomerization domain. J Struct Biol 2016; 193:141-54. [DOI: 10.1016/j.jsb.2015.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/13/2015] [Accepted: 12/06/2015] [Indexed: 01/23/2023]
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7
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Healy EF. A model for non-obligate oligomer formation in protein aggregration. Biochem Biophys Res Commun 2015; 465:523-7. [PMID: 26282203 PMCID: PMC4564312 DOI: 10.1016/j.bbrc.2015.08.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022]
Abstract
Using solvent-exposed intramolecular backbone hydrogen bonds as physico-chemical descriptors for protein packing, a role for transient, non-obligate oligomers in the formation of aberrant protein aggregates is presented. Oligomeric models of the both wild type (wt) and select mutant variants of superoxide dismutase (SOD1) are proposed to provide a structural basis for investigating the etiology of Amyotrophic Lateral Sclerosis (ALS).
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Affiliation(s)
- Eamonn F Healy
- Department of Chemistry, St. Edward's University, Austin, TX 78704, USA.
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8
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Walsh G. Protein Purification and Characterization. Proteins 2015. [DOI: 10.1002/9781119117599.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Gupta K, Zamanian M, Bae C, Milescu M, Krepkiy D, Tilley DC, Sack JT, Yarov-Yarovoy V, Kim JI, Swartz KJ. Tarantula toxins use common surfaces for interacting with Kv and ASIC ion channels. eLife 2015; 4:e06774. [PMID: 25948544 PMCID: PMC4423116 DOI: 10.7554/elife.06774] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/16/2015] [Indexed: 12/14/2022] Open
Abstract
Tarantula toxins that bind to voltage-sensing domains of voltage-activated ion channels are thought to partition into the membrane and bind to the channel within the bilayer. While no structures of a voltage-sensor toxin bound to a channel have been solved, a structural homolog, psalmotoxin (PcTx1), was recently crystalized in complex with the extracellular domain of an acid sensing ion channel (ASIC). In the present study we use spectroscopic, biophysical and computational approaches to compare membrane interaction properties and channel binding surfaces of PcTx1 with the voltage-sensor toxin guangxitoxin (GxTx-1E). Our results show that both types of tarantula toxins interact with membranes, but that voltage-sensor toxins partition deeper into the bilayer. In addition, our results suggest that tarantula toxins have evolved a similar concave surface for clamping onto α-helices that is effective in aqueous or lipidic physical environments.
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Affiliation(s)
- Kanchan Gupta
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institutes of Health, Bethesda, United States
| | - Maryam Zamanian
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institutes of Health, Bethesda, United States
| | - Chanhyung Bae
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institutes of Health, Bethesda, United States
| | - Mirela Milescu
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institutes of Health, Bethesda, United States
| | - Dmitriy Krepkiy
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institutes of Health, Bethesda, United States
| | - Drew C Tilley
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
| | - Jon T Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
| | - Jae Il Kim
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institutes of Health, Bethesda, United States
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Kamnesky G, Hirschhorn O, Shaked H, Chen J, Yao L, Chill JH. Molecular determinants of tetramerization in the KcsA cytoplasmic domain. Protein Sci 2014; 23:1403-16. [PMID: 25042120 DOI: 10.1002/pro.2525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/11/2022]
Abstract
The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels.
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Affiliation(s)
- Guy Kamnesky
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
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Soluble adenylyl cyclase in health and disease. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2584-92. [PMID: 25064591 DOI: 10.1016/j.bbadis.2014.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/12/2014] [Accepted: 07/15/2014] [Indexed: 12/14/2022]
Abstract
The second messenger cAMP is integral for many physiological processes. Soluble adenylyl cyclase (sAC) was recently identified as a widely expressed intracellular source of cAMP in mammalian cells. sAC is evolutionary, structurally, and biochemically distinct from the G-protein-responsive transmembranous adenylyl cyclases (tmAC). The structure of the catalytic unit of sAC is similar to tmAC, but sAC does not contain transmembranous domains, allowing localizations independent of the membranous compartment. sAC activity is stimulated by HCO(3)(-), Ca²⁺ and is sensitive to physiologically relevant ATP fluctuations. sAC functions as a physiological sensor for carbon dioxide and bicarbonate, and therefore indirectly for pH. Here we review the physiological role of sAC in different human tissues with a major focus on the lung. This article is part of a Special Issue entitled: The role of soluble adenylyl cyclase in health and disease, guest edited by J. Buck and L.R. Levin.
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Billaud M, Lohman AW, Johnstone SR, Biwer LA, Mutchler S, Isakson BE. Regulation of cellular communication by signaling microdomains in the blood vessel wall. Pharmacol Rev 2014; 66:513-69. [PMID: 24671377 DOI: 10.1124/pr.112.007351] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It has become increasingly clear that the accumulation of proteins in specific regions of the plasma membrane can facilitate cellular communication. These regions, termed signaling microdomains, are found throughout the blood vessel wall where cellular communication, both within and between cell types, must be tightly regulated to maintain proper vascular function. We will define a cellular signaling microdomain and apply this definition to the plethora of means by which cellular communication has been hypothesized to occur in the blood vessel wall. To that end, we make a case for three broad areas of cellular communication where signaling microdomains could play an important role: 1) paracrine release of free radicals and gaseous molecules such as nitric oxide and reactive oxygen species; 2) role of ion channels including gap junctions and potassium channels, especially those associated with the endothelium-derived hyperpolarization mediated signaling, and lastly, 3) mechanism of exocytosis that has considerable oversight by signaling microdomains, especially those associated with the release of von Willebrand factor. When summed, we believe that it is clear that the organization and regulation of signaling microdomains is an essential component to vessel wall function.
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Affiliation(s)
- Marie Billaud
- Dept. of Molecular Physiology and Biophysics, University of Virginia School of Medicine, PO Box 801394, Charlottesville, VA 22902.
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Crystal structures of human soluble adenylyl cyclase reveal mechanisms of catalysis and of its activation through bicarbonate. Proc Natl Acad Sci U S A 2014; 111:3727-32. [PMID: 24567411 DOI: 10.1073/pnas.1322778111] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
cAMP is an evolutionary conserved, prototypic second messenger regulating numerous cellular functions. In mammals, cAMP is synthesized by one of 10 homologous adenylyl cyclases (ACs): nine transmembrane enzymes and one soluble AC (sAC). Among these, only sAC is directly activated by bicarbonate (HCO3(-)); it thereby serves as a cellular sensor for HCO3(-), carbon dioxide (CO2), and pH in physiological functions, such as sperm activation, aqueous humor formation, and metabolic regulation. Here, we describe crystal structures of human sAC catalytic domains in the apo state and in complex with substrate analog, products, and regulators. The activator HCO3(-) binds adjacent to Arg176, which acts as a switch that enables formation of the catalytic cation sites. An anionic inhibitor, 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid, inhibits sAC through binding to the active site entrance, which blocks HCO3(-) activation through steric hindrance and trapping of the Arg176 side chain. Finally, product complexes reveal small, local rearrangements that facilitate catalysis. Our results provide a molecular mechanism for sAC catalysis and cellular HCO3(-) sensing and a basis for targeting this system with drugs.
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Alocci D, Bernini A, Niccolai N. Atom depth analysis delineates mechanisms of protein intermolecular interactions. Biochem Biophys Res Commun 2013; 436:725-9. [PMID: 23791741 DOI: 10.1016/j.bbrc.2013.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 06/09/2013] [Indexed: 10/26/2022]
Abstract
The systematic analysis of amino acid distribution, performed inside a large set of resolved protein structures, sheds light on possible mechanisms driving non random protein-protein approaches. Protein Data Bank entries have been selected using as filters a series of restrictions ensuring that the shape of protein surface is not modified by interactions with large or small ligands. 3D atom depth has been evaluated for all the atoms of the 2,410 selected structures. The amino acid relative population in each of the structural layers formed by grouping atoms on the basis of their calculated depths, has been evaluated. We have identified seven structural layers, the inner ones reproducing the core of proteins and the outer one incorporating their most protruding moieties. Quantitative analysis of amino acid contents of structural layers identified, as expected, different behaviors. Atoms of Q, R, K, N, D residues are increasingly more abundant in going from core to surfaces. An opposite trend is observed for V, I, L, A, C, and G. An intermediate behavior is exhibited by P, S, T, M, W, H, F and Y. The outer structural layer hosts predominantly E and K residues whose charged moieties, protruding from outer regions of the protein surface, reorient free from steric hindrances, determining specific electrodynamics maps. This feature may represent a protein signature for long distance effects, driving the formation of encounter complexes and the eventual short distance approaches that are required for protein-protein functional interactions.
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Affiliation(s)
- Davide Alocci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena, Italy.
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