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Article: Ionization Properties of Phospholipids Determined by Zeta Potential Measurements.

Sathappa, Murugappan / Alder, Nathan N

2016 Volume 6, Issue 22

Abstract: Biological membranes are vital for diverse cellular functions such as maintaining cell and organelle structure, selective permeability, active transport, and signaling. The surface charge of the membrane bilayer plays a critical role in these myriad ... ...

Abstract	Biological membranes are vital for diverse cellular functions such as maintaining cell and organelle structure, selective permeability, active transport, and signaling. The surface charge of the membrane bilayer plays a critical role in these myriad processes. For most biomembranes, the surface charge of anionic phospholipids contributes to the negative surface charge density within the interfacial region of the bilayer. To quantify surface charge, it is essential to understand the proton dissociation behavior of the titratable headgroups within such lipids. We describe a protocol that uses model membranes for electrokinetic zeta potential measurements coupled with data analysis using Gouy-Chapman-Stern formalism to determine the p
Language	English
Publishing date	2016-12-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.e2030
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Article: The ionization properties of cardiolipin and its variants in model bilayers.

Sathappa, Murugappan / Alder, Nathan N

Biochimica et biophysica acta

2016 Volume 1858, Issue 6, Page(s) 1362–1372

Abstract: The anionic phospholipid cardiolipin has an unusual dimeric structure with a two-phosphate headgroup and four acyl chains. Cardiolipin is present in energy-transducing membranes that maintain electrochemical gradients, including most bacterial plasma ... ...

Abstract	The anionic phospholipid cardiolipin has an unusual dimeric structure with a two-phosphate headgroup and four acyl chains. Cardiolipin is present in energy-transducing membranes that maintain electrochemical gradients, including most bacterial plasma membranes and the mitochondrial inner membrane, where it mediates respiratory complex assembly and activation, among many other roles. Dysfunctional biogenesis of cardiolipin is implicated in the pathogenesis of several diseases including Barth syndrome. Because cardiolipin is a dominant anionic lipid in energy-conserving membranes, its headgroup is a major contributor to surface charge density and the bilayer electrostatic profile. However, the proton dissociation behavior of its headgroup remains controversial. In one model, the pKa values of the phosphates differ by several units and the headgroup exists as a monoanion at physiological pH. In another model, both phosphates ionize as strong acids with low pKa values and the headgroup exists in dianionic form at physiological pH. Using independent electrokinetic and spectroscopic approaches, coupled with analysis using Gouy-Chapman-Stern formalism, we have analyzed the ionization properties of cardiolipin within biologically relevant lipid bilayer model systems. We show that both phosphates of the cardiolipin headgroup show strong ionization behavior with low pKa values. Moreover, cardiolipin variants lacking structural features proposed to be required to maintain disparate pKa values--namely the secondary hydroxyl on the central glycerol or a full complement of four acyl chains--were shown to have ionization behavior identical to intact cardiolipin. Hence, these results indicate that within the physiological pH range, the cardiolipin headgroup is fully ionized as a dianion. We discuss the implications of these results with respect to the role of cardiolipin in defining membrane surface potential, activating respiratory complexes, and modulating membrane curvature.
MeSH term(s)	Cardiolipins/chemistry ; Hydrogen-Ion Concentration ; Ions ; Lipid Bilayers ; Models, Chemical ; Static Electricity
Chemical Substances	Cardiolipins ; Ions ; Lipid Bilayers
Language	English
Publishing date	2016-03-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamem.2016.03.007
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Article ; Online: The mitochondria-targeted peptide SS-31 binds lipid bilayers and modulates surface electrostatics as a key component of its mechanism of action.

Mitchell, Wayne / Ng, Emily A / Tamucci, Jeffrey D / Boyd, Kevin J / Sathappa, Murugappan / Coscia, Adrian / Pan, Meixia / Han, Xianlin / Eddy, Nicholas A / May, Eric R / Szeto, Hazel H / Alder, Nathan N

The Journal of biological chemistry

2020 Volume 295, Issue 21, Page(s) 7452–7469

Abstract: Mitochondrial dysfunction underlies many heritable diseases, acquired pathologies, and aging-related declines in health. Szeto-Schiller (SS) peptides comprise a class of amphipathic tetrapeptides that are efficacious toward a wide array of mitochondrial ... ...

Abstract	Mitochondrial dysfunction underlies many heritable diseases, acquired pathologies, and aging-related declines in health. Szeto-Schiller (SS) peptides comprise a class of amphipathic tetrapeptides that are efficacious toward a wide array of mitochondrial disorders and are believed to target mitochondrial membranes because they are enriched in the anionic phospholipid cardiolipin (CL). However, little is known regarding how SS peptides interact with or alter the physical properties of lipid bilayers. In this study, using biophysical and computational approaches, we have analyzed the interactions of the lead compound SS-31 (elamipretide) with model and mitochondrial membranes. Our results show that this polybasic peptide partitions into the membrane interfacial region with an affinity and a lipid binding density that are directly related to surface charge. We found that SS-31 binding does not destabilize lamellar bilayers even at the highest binding concentrations; however, it did cause saturable alterations in lipid packing. Most notably, SS-31 modulated the surface electrostatics of both model and mitochondrial membranes. We propose nonexclusive mechanisms by which the tuning of surface charge could underpin the mitoprotective properties of SS-31, including alteration of the distribution of ions and basic proteins at the interface, and/or modulation of bilayer physical properties. As a proof of concept, we show that SS-31 alters divalent cation (calcium) distribution within the interfacial region and reduces the energetic burden of calcium stress in mitochondria. The mechanistic details of SS-31 revealed in this study will help inform the development of future compound variants with enhanced efficacy and bioavailability.
MeSH term(s)	Calcium/metabolism ; Lipid Bilayers/chemistry ; Mitochondria/metabolism ; Oligopeptides/chemistry ; Saccharomyces cerevisiae/metabolism ; Static Electricity
Chemical Substances	Lipid Bilayers ; Oligopeptides ; arginyl-2,'6'-dimethyltyrosyl-lysyl-phenylalaninamide ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2020-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA119.012094
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Article ; Online: Allosteric inhibition of PPM1D serine/threonine phosphatase via an altered conformational state.

Miller, Peter G / Sathappa, Murugappan / Moroco, Jamie A / Jiang, Wei / Qian, Yue / Iqbal, Sumaiya / Guo, Qi / Giacomelli, Andrew O / Shaw, Subrata / Vernier, Camille / Bajrami, Besnik / Yang, Xiaoping / Raffier, Cerise / Sperling, Adam S / Gibson, Christopher J / Kahn, Josephine / Jin, Cyrus / Ranaghan, Matthew / Caliman, Alisha /

Brousseau, Merissa / Fischer, Eric S / Lintner, Robert / Piccioni, Federica / Campbell, Arthur J / Root, David E / Garvie, Colin W / Ebert, Benjamin L

Nature communications

2022 Volume 13, Issue 1, Page(s) 3778

Abstract: PPM1D encodes a serine/threonine phosphatase that regulates numerous pathways including the DNA damage response and p53. Activating mutations and amplification of PPM1D are found across numerous cancer types. GSK2830371 is a potent and selective ... ...

Abstract	PPM1D encodes a serine/threonine phosphatase that regulates numerous pathways including the DNA damage response and p53. Activating mutations and amplification of PPM1D are found across numerous cancer types. GSK2830371 is a potent and selective allosteric inhibitor of PPM1D, but its mechanism of binding and inhibition of catalytic activity are unknown. Here we use computational, biochemical and functional genetic studies to elucidate the molecular basis of GSK2830371 activity. These data confirm that GSK2830371 binds an allosteric site of PPM1D with high affinity. By further incorporating data from hydrogen deuterium exchange mass spectrometry and sedimentation velocity analytical ultracentrifugation, we demonstrate that PPM1D exists in an equilibrium between two conformations that are defined by the movement of the flap domain, which is required for substrate recognition. A hinge region was identified that is critical for switching between the two conformations and was directly implicated in the high-affinity binding of GSK2830371 to PPM1D. We propose that the two conformations represent active and inactive forms of the protein reflected by the position of the flap, and that binding of GSK2830371 shifts the equilibrium to the inactive form. Finally, we found that C-terminal truncating mutations proximal to residue 400 result in destabilization of the protein via loss of a stabilizing N- and C-terminal interaction, consistent with the observation from human genetic data that nearly all PPM1D mutations in cancer are truncating and occur distal to residue 400. Taken together, our findings elucidate the mechanism by which binding of a small molecule to an allosteric site of PPM1D inhibits its activity and provides insights into the biology of PPM1D.
MeSH term(s)	Allosteric Site ; Aminopyridines/pharmacology ; Dipeptides/pharmacology ; Humans ; Mutation ; Neoplasms/drug therapy ; Neoplasms/enzymology ; Neoplasms/genetics ; Protein Conformation ; Protein Phosphatase 2C/antagonists & inhibitors ; Protein Phosphatase 2C/chemistry ; Protein Phosphatase 2C/genetics ; Protein Phosphatase 2C/metabolism ; Serine/genetics ; Serine/metabolism ; Structure-Activity Relationship
Chemical Substances	Aminopyridines ; Dipeptides ; GSK2830371 ; Serine (452VLY9402) ; PPM1D protein, human (EC 3.1.3.16) ; Protein Phosphatase 2C (EC 3.1.3.16)
Language	English
Publishing date	2022-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-30463-9
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Article ; Online: Allosteric inhibition of PPM1D serine/threonine phosphatase via an altered conformational state

Peter G. Miller / Murugappan Sathappa / Jamie A. Moroco / Wei Jiang / Yue Qian / Sumaiya Iqbal / Qi Guo / Andrew O. Giacomelli / Subrata Shaw / Camille Vernier / Besnik Bajrami / Xiaoping Yang / Cerise Raffier / Adam S. Sperling / Christopher J. Gibson / Josephine Kahn / Cyrus Jin / Matthew Ranaghan / Alisha Caliman /

Merissa Brousseau / Eric S. Fischer / Robert Lintner / Federica Piccioni / Arthur J. Campbell / David E. Root / Colin W. Garvie / Benjamin L. Ebert

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 16

Abstract: In this work, the authors report a sophisticated combination of genetic, biophysical, and biochemical analyses to identifies the cycling conformational states of PPM1D. The findings reveal how an allosteric inhibitor locks the protein into a ... ...

Abstract	In this work, the authors report a sophisticated combination of genetic, biophysical, and biochemical analyses to identifies the cycling conformational states of PPM1D. The findings reveal how an allosteric inhibitor locks the protein into a conformationally inactive state, and explain the distribution of PPM1D activating mutations in cancer.
Keywords	Science ; Q
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structural changes in the mitochondrial Tim23 channel are coupled to the proton-motive force.

Malhotra, Ketan / Sathappa, Murugappan / Landin, Judith S / Johnson, Arthur E / Alder, Nathan N

Nature structural & molecular biology

2013 Volume 20, Issue 8, Page(s) 965–972

Abstract: Tim23, the central subunit of the TIM23 protein-translocation complex, forms a voltage-gated channel in the mitochondrial inner membrane (MIM), an energy-conserving membrane that generates a proton-motive force to drive vital processes. Using high- ... ...

Abstract	Tim23, the central subunit of the TIM23 protein-translocation complex, forms a voltage-gated channel in the mitochondrial inner membrane (MIM), an energy-conserving membrane that generates a proton-motive force to drive vital processes. Using high-resolution fluorescence mapping of a channel-facing transmembrane segment (TMS2) of Tim23 from Saccharomyces cerevisiae, we demonstrate that changes in the energized state of the MIM cause marked structural alterations in the channel region. In an energized membrane, TMS2 forms a continuous α-helix that is inaccessible to the aqueous intermembrane space (IMS). Upon depolarization, the helical periodicity of TMS2 is disrupted, and the channel becomes exposed to the IMS. Kinetic measurements confirm that changes in TMS2 conformation coincide with depolarization. These results reveal how the energized state of the membrane drives functionally relevant structural dynamics in membrane proteins coupled to processes such as channel gating.
MeSH term(s)	Amino Acid Sequence ; Cloning, Molecular ; Kinetics ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/metabolism ; Microscopy, Fluorescence ; Mitochondrial Membranes/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multiprotein Complexes/chemistry ; Multiprotein Complexes/metabolism ; Protein Structure, Secondary ; Proton-Motive Force/physiology ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Alignment
Chemical Substances	Membrane Transport Proteins ; Multiprotein Complexes ; Saccharomyces cerevisiae Proteins ; TIM23 protein, S cerevisiae
Language	English
Publishing date	2013-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb.2613
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Article ; Online: Multimodal small-molecule screening for human prion protein binders.

Reidenbach, Andrew G / Mesleh, Michael F / Casalena, Dominick / Vallabh, Sonia M / Dahlin, Jayme L / Leed, Alison J / Chan, Alix I / Usanov, Dmitry L / Yehl, Jenna B / Lemke, Christopher T / Campbell, Arthur J / Shah, Rishi N / Shrestha, Om K / Sacher, Joshua R / Rangel, Victor L / Moroco, Jamie A / Sathappa, Murugappan / Nonato, Maria Cristina / Nguyen, Kong T /

Wright, S Kirk / Liu, David R / Wagner, Florence F / Kaushik, Virendar K / Auld, Douglas S / Schreiber, Stuart L / Minikel, Eric Vallabh

The Journal of biological chemistry

2020 Volume 295, Issue 39, Page(s) 13516–13531

Abstract: Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting ... ...

Abstract	Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including
MeSH term(s)	Benzimidazoles/chemistry ; Benzimidazoles/pharmacology ; Drug Discovery ; Drug Evaluation, Preclinical ; Humans ; Magnetic Resonance Spectroscopy ; Prion Diseases/drug therapy ; Prion Diseases/metabolism ; Prion Proteins/antagonists & inhibitors ; Prion Proteins/metabolism ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology
Chemical Substances	Benzimidazoles ; Prion Proteins ; Small Molecule Libraries ; benzimidazole (E24GX49LD8)
Language	English
Publishing date	2020-07-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA120.014905
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Article ; Online: Unremodeled and remodeled cardiolipin are functionally indistinguishable in yeast.

Baile, Matthew G / Sathappa, Murugappan / Lu, Ya-Wen / Pryce, Erin / Whited, Kevin / McCaffery, J Michael / Han, Xianlin / Alder, Nathan N / Claypool, Steven M

The Journal of biological chemistry

2013 Volume 289, Issue 3, Page(s) 1768–1778

Abstract: After biosynthesis, an evolutionarily conserved acyl chain remodeling process generates a final highly homogeneous and yet tissue-specific molecular form of the mitochondrial lipid cardiolipin. Hence, cardiolipin molecules in different organisms, and ... ...

Abstract	After biosynthesis, an evolutionarily conserved acyl chain remodeling process generates a final highly homogeneous and yet tissue-specific molecular form of the mitochondrial lipid cardiolipin. Hence, cardiolipin molecules in different organisms, and even different tissues within the same organism, contain a distinct collection of attached acyl chains. This observation is the basis for the widely accepted paradigm that the acyl chain composition of cardiolipin is matched to the unique mitochondrial demands of a tissue. For this hypothesis to be correct, cardiolipin molecules with different acyl chain compositions should have distinct functional capacities, and cardiolipin that has been remodeled should promote cardiolipin-dependent mitochondrial processes better than its unremodeled form. However, functional disparities between different molecular forms of cardiolipin have never been established. Here, we interrogate this simple but crucial prediction utilizing the best available model to do so, Saccharomyces cerevisiae. Specifically, we compare the ability of unremodeled and remodeled cardiolipin, which differ markedly in their acyl chain composition, to support mitochondrial activities known to require cardiolipin. Surprisingly, defined changes in the acyl chain composition of cardiolipin do not alter either mitochondrial morphology or oxidative phosphorylation. Importantly, preventing cardiolipin remodeling initiation in yeast lacking TAZ1, an ortholog of the causative gene in Barth syndrome, ameliorates mitochondrial dysfunction. Thus, our data do not support the prevailing hypothesis that unremodeled cardiolipin is functionally distinct from remodeled cardiolipin, at least for the functions examined, suggesting alternative physiological roles for this conserved pathway.
MeSH term(s)	Acyltransferases/genetics ; Acyltransferases/metabolism ; Barth Syndrome/genetics ; Barth Syndrome/metabolism ; Cardiolipins/genetics ; Cardiolipins/metabolism ; Gene Deletion ; Humans ; Mitochondria/genetics ; Mitochondria/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Cardiolipins ; Saccharomyces cerevisiae Proteins ; Transcription Factors ; Acyltransferases (EC 2.3.-) ; Taz1 protein, S cerevisiae (EC 2.3.-) ; TAFAZZIN protein, human (EC 2.3.1.-)
Language	English
Publishing date	2013-11-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M113.525733
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Article: Multimodal small-molecule screening for human prion protein binders

Wright, S Kirk / Liu, David R / Wagner, Florence F / Kaushik, Virendar K / Auld, Douglas S / Schreiber, Stuart L / Minikel, Eric Vallabh

J. biol. chem

Abstract	Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19F-observed and saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, and in silico screening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (K d > 1 mM), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. While orthogonal binder discovery methods could yield high affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #32723867
Database	COVID19

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