Nur Alia Oktaviani - Academia.edu (original) (raw)

Papers by Nur Alia Oktaviani

Chemical Communications, 2019

Chaotropic ions prevent molecular interactions of a spider silk protein, which are required to ma... more Chaotropic ions prevent molecular interactions of a spider silk protein, which are required to maintain the solubility, while kosmotropic ions promote hydrogen bond interactions, which are a prerequisite for β-sheet formation.

Oktaviani, N. (2014). NMR studies of folded and unfolded proteins: method developments and biolog... more Oktaviani, N. (2014). NMR studies of folded and unfolded proteins: method developments and biological insight. s.n.

Biophysical Journal, 2017

Take-down policy If you believe that this document breaches copyright please contact us providing... more Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

Angewandte Chemie, 2016

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Journal of Biomolecular NMR, 2015

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisi... more Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

International Journal of Pharmaceutics, 2013

Oxytocin is a peptide drug used to induce labor and prevent bleeding after childbirth. Due to its... more Oxytocin is a peptide drug used to induce labor and prevent bleeding after childbirth. Due to its instability, transport and storage of oxytocin formulations under tropical conditions is problematic. In a previous study, we have found that the stability of oxytocin in aspartate buffered formulation is improved by the addition of divalent metal ions (unpublished results). The stabilizing effect of Zn 2+ was by far superior compared to that of Mg 2+. In addition, it was found that stabilization correlated well with the ability of the divalent metal ions to interact with oxytocin in aspartate buffer. Furthermore, LC-MS (MS) measurements indicated that the combination of aspartate buffer and Zn 2+ in particular suppressed intermolecular degradation reactions near the Cys 1,6 disulfide bridge. These results lead to the hypothesis that in aspartate buffer, Zn 2+ changes the conformation of oxytocin in such a way that the Cys 1,6 disulfide bridge is shielded from its environment thereby suppressing intermolecular reactions involving this region of the molecule. To verify this hypothesis, we investigate here the conformation of oxytocin in aspartate buffer in the presence of Mg 2+ or Zn 2+ , using 2D NOESY, TOCSY, 1 H-13 C HSQC and 1 H-15 N HSQC NMR spectroscopy. Almost all 1 H, 13 C and 15 N resonances of oxytocin could be assigned using HSQC spectroscopy, without the need for 13 C or 15 N enrichment. 1 H-13 C and 1 H-15 N HSQC spectra showed that aspartate buffer alone induces minor changes in oxytocin in D 2 O, with the largest chemical shift changes observed for Cys 1. Zn 2+ causes more extensive changes in oxytocin in aqueous solution than Mg 2+. Our findings suggest that the carboxylate group of aspartate neutralizes the positive charge of the N-terminus of Cys 1 , allowing the interactions with Zn 2+ to become more favorable. These interactions may explain the protection of the disulfide bridge against intermolecular reactions that lead to dimerization.

Biochemical Journal, 2014

We demonstrate that certain covalently cross-linked Aβ dimers have subtly different structural pr... more We demonstrate that certain covalently cross-linked Aβ dimers have subtly different structural propensities and aggregate by pathways distinct from that of monomers. These differences lead to the prolonged presence of bioactive soluble assemblies that may contribute to Alzheimer's disease pathogenesis.

Biomolecular NMR Assignments, 2010

Here we present the 100% complete assignment chemical shift of non-labile 1 H, 15 N and 13 C nucl... more Here we present the 100% complete assignment chemical shift of non-labile 1 H, 15 N and 13 C nuclei of Calbindin D 9k P43G. The assignment includes all nonexchangeable side chain nuclei, including ones that are rarely reported, such as LysNf as well as the termini. NMR experiments required to achieve truly complete assignments are discussed. To the best of our knowledge our assignments for Calbindin D 9k extend beyond previous studies reaching near-completeness (

Biomolecular NMR Assignments, 2012

Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue li... more Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue light of the bacterium Halorhodospira halophila. Here, we report nearly complete backbone and side chain 1 H, 13 C and 15 N resonance assignments at pH 5.8 and 20°C of PYP in its electronic ground state. Keywords PYP Á Halorhodospira halophila Á paracoumaric acid Á NMR spectroscopy Á Photoactivation Biological context Photoactive yellow protein (PYP) is a 125 amino acid (14 kDa) water-soluble, blue-light sensor protein, first found in the halophilic bacterium Halorhodospira halophila (Meyer 1985). PYP is a photoreceptor, believed to be responsible for the negative phototactic response of its host organism (Sprenger et al. 1993). This kind of response is required for organisms to evade potentially harmful short-wavelength light. Based on this observation, PYP has become a suitable model to understand the signal-transduction mechanism in Per-Arnt-Sim (PAS) domain signaling (Crosthwaite et al. 1997; Nambu et al. 1991). Several PYP-like proteins have meanwhile been found in other organisms, where they are also thought to act as light sensors. In addition, PYP-like proteins found in purple bacteria are involved in cell buoyancy or sensing bacteriophytochromes (Jiang et al. 1999; Kyndt et al. 2004). Understanding of light transduction in PYP requires structural information in atomic detail. A 1.4 Å crystallographic structure was determined in 1995 by Borgstahl et al. and in 1998 Düx and coworkers revealed the solution structure and backbone dynamics of PYP by NMR spectroscopy. The reaction center of PYP is protected from solvent by R52, which is believed to function as a gateway in the photocycle (Borgstahl et al. 1995; Genick et al. 1997). The chromophore, para-coumaric acid (pCA), is covalenty bound to C69 with a thioester bond and pCA participates in two short hydrogen bonds with E46 and Y42 to stabilize the negative charge of pCA in the electronic ground state, pG. Upon blue-light capture, the chromophore undergoes transcis isomerisation and the intermediate pR is formed, which subsequently relaxes to the proposed signaling state, pB. In the latter state, the reaction center is exposed and the two short hydrogen bonds are broken (Borgstahl et al. 1995; Sigala et al. 2009; Yamaguchi et al. 2009). In this paper, we present the nearly complete assignment of the backbone and side chain resonances of the pG state of PYP. Methods and experiments Uniformly 13 C, 15 N-labeled wild type PYP was overexpressed and purified as described previously (Düx et al.

Biophysical Journal, 2012

Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activ... more Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activity of its flagellar motor and thereby evade potentially harmful UV radiation. The 14 kDa soluble cytosolic photoactive yellow protein (PYP) is believed to be the primary mediator of this photophobic response, and yields a UV/Vis absorption spectrum that closely matches the bacterium's motility spectrum. In the electronic ground state, the para-coumaric acid (pCA) chromophore of PYP is negatively charged and forms two short hydrogen bonds to the side chains of Glu-46 and Tyr-42. The resulting acid triad is central to the marked pH dependence of the optical-absorption relaxation kinetics of PYP. Here, we describe an NMR approach to sequence-specifically follow all tyrosine side-chain protonation states in PYP from pH 3.41 to 11.24. The indirect observation of the nonprotonated 13 C g resonances in sensitive and well-resolved two-dimensional 13 C-1 H spectra proved to be pivotal in this effort, as observation of other ring-system resonances was hampered by spectral congestion and line-broadening due to ring flips. We observe three classes of tyrosine residues in PYP that exhibit very different pK a values depending on whether the phenolic side chain is solvent-exposed, buried, or hydrogen-bonded. In particular, our data show that Tyr-42 remains fully protonated in the pH range of 3.41-11.24, and that pH-induced changes observed in the photocycle kinetics of PYP cannot be caused by changes in the charge state of Tyr-42. It is therefore very unlikely that the pCA chromophore undergoes changes in its electrostatic interactions in the electronic ground state.

Biomacromolecules, 2022

The tiny spider makes dragline silk fibers with unbeatable toughness, all under the most innocuou... more The tiny spider makes dragline silk fibers with unbeatable toughness, all under the most innocuous conditions. Scientists have persistently tried to emulate its natural silk spinning process using recombinant proteins with a view toward creating a new wave of smart materials, yet most efforts have fallen short of attaining the native fiber's excellent mechanical properties. One reason for these shortcomings may be that artificial spider silk systems tend to be overly simplified and may not sufficiently take into account the true complexity of the underlying protein sequences and of the multidimensional aspects of the natural self-assembly process that give rise to the hierarchically structured fibers. Here, we discuss recent findings regarding the material constituents of spider dragline silk, including novel spidroin subtypes, nonspidroin proteins, and possible involvement of post-translational modifications, which together suggest a complexity that transcends the two-component MaSp1/MaSp2 system. We subsequently consider insights into the spidroin domain functions, structures, and overall mechanisms for the rapid transition from disordered soluble protein into a highly organized fiber, including the possibility of viewing spider silk self-assembly through a framework relevant to biomolecular condensates. Finally, we consider the concept of "biomimetics" as it applies to artificial spider silk production with a focus on key practical aspects of design and evaluation that may hopefully inform efforts to more closely reproduce the remarkable structure and function of the native silk fiber using artificial methods.

Protein Science, 2009

Lactococcus lactis is a promising host for (membrane) protein overproduction. Here, we describe a... more Lactococcus lactis is a promising host for (membrane) protein overproduction. Here, we describe a protocol for incorporation of selenomethionine (SeMet) into proteins expressed in L. lactis. Incorporation efficiencies of SeMet in the membrane protein complex OpuA (an ABC transporter) and the soluble protein OppA, both from L. lactis, were monitored by mass spectrometry. Both proteins incorporated SeMet with high efficiencies (>90%), which greatly extends the usefulness of the expression host L. lactis for X-ray crystallography purposes. The crystal structure of ligand-free OppA was determined at 2.4 Å resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing.

Chemical Communications, 2019

Chaotropic ions prevent molecular interactions of a spider silk protein, which are required to ma... more Chaotropic ions prevent molecular interactions of a spider silk protein, which are required to maintain the solubility, while kosmotropic ions promote hydrogen bond interactions, which are a prerequisite for β-sheet formation.

Oktaviani, N. (2014). NMR studies of folded and unfolded proteins: method developments and biolog... more Oktaviani, N. (2014). NMR studies of folded and unfolded proteins: method developments and biological insight. s.n.

Biophysical Journal, 2017

Take-down policy If you believe that this document breaches copyright please contact us providing... more Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

Angewandte Chemie, 2016

Take-down policy If you believe that this document breaches copyright please contact us providing... more Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

Journal of Biomolecular NMR, 2015

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisi... more Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

International Journal of Pharmaceutics, 2013

Oxytocin is a peptide drug used to induce labor and prevent bleeding after childbirth. Due to its... more Oxytocin is a peptide drug used to induce labor and prevent bleeding after childbirth. Due to its instability, transport and storage of oxytocin formulations under tropical conditions is problematic. In a previous study, we have found that the stability of oxytocin in aspartate buffered formulation is improved by the addition of divalent metal ions (unpublished results). The stabilizing effect of Zn 2+ was by far superior compared to that of Mg 2+. In addition, it was found that stabilization correlated well with the ability of the divalent metal ions to interact with oxytocin in aspartate buffer. Furthermore, LC-MS (MS) measurements indicated that the combination of aspartate buffer and Zn 2+ in particular suppressed intermolecular degradation reactions near the Cys 1,6 disulfide bridge. These results lead to the hypothesis that in aspartate buffer, Zn 2+ changes the conformation of oxytocin in such a way that the Cys 1,6 disulfide bridge is shielded from its environment thereby suppressing intermolecular reactions involving this region of the molecule. To verify this hypothesis, we investigate here the conformation of oxytocin in aspartate buffer in the presence of Mg 2+ or Zn 2+ , using 2D NOESY, TOCSY, 1 H-13 C HSQC and 1 H-15 N HSQC NMR spectroscopy. Almost all 1 H, 13 C and 15 N resonances of oxytocin could be assigned using HSQC spectroscopy, without the need for 13 C or 15 N enrichment. 1 H-13 C and 1 H-15 N HSQC spectra showed that aspartate buffer alone induces minor changes in oxytocin in D 2 O, with the largest chemical shift changes observed for Cys 1. Zn 2+ causes more extensive changes in oxytocin in aqueous solution than Mg 2+. Our findings suggest that the carboxylate group of aspartate neutralizes the positive charge of the N-terminus of Cys 1 , allowing the interactions with Zn 2+ to become more favorable. These interactions may explain the protection of the disulfide bridge against intermolecular reactions that lead to dimerization.

Biochemical Journal, 2014

We demonstrate that certain covalently cross-linked Aβ dimers have subtly different structural pr... more We demonstrate that certain covalently cross-linked Aβ dimers have subtly different structural propensities and aggregate by pathways distinct from that of monomers. These differences lead to the prolonged presence of bioactive soluble assemblies that may contribute to Alzheimer's disease pathogenesis.

Biomolecular NMR Assignments, 2010

Here we present the 100% complete assignment chemical shift of non-labile 1 H, 15 N and 13 C nucl... more Here we present the 100% complete assignment chemical shift of non-labile 1 H, 15 N and 13 C nuclei of Calbindin D 9k P43G. The assignment includes all nonexchangeable side chain nuclei, including ones that are rarely reported, such as LysNf as well as the termini. NMR experiments required to achieve truly complete assignments are discussed. To the best of our knowledge our assignments for Calbindin D 9k extend beyond previous studies reaching near-completeness (

Biomolecular NMR Assignments, 2012

Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue li... more Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue light of the bacterium Halorhodospira halophila. Here, we report nearly complete backbone and side chain 1 H, 13 C and 15 N resonance assignments at pH 5.8 and 20°C of PYP in its electronic ground state. Keywords PYP Á Halorhodospira halophila Á paracoumaric acid Á NMR spectroscopy Á Photoactivation Biological context Photoactive yellow protein (PYP) is a 125 amino acid (14 kDa) water-soluble, blue-light sensor protein, first found in the halophilic bacterium Halorhodospira halophila (Meyer 1985). PYP is a photoreceptor, believed to be responsible for the negative phototactic response of its host organism (Sprenger et al. 1993). This kind of response is required for organisms to evade potentially harmful short-wavelength light. Based on this observation, PYP has become a suitable model to understand the signal-transduction mechanism in Per-Arnt-Sim (PAS) domain signaling (Crosthwaite et al. 1997; Nambu et al. 1991). Several PYP-like proteins have meanwhile been found in other organisms, where they are also thought to act as light sensors. In addition, PYP-like proteins found in purple bacteria are involved in cell buoyancy or sensing bacteriophytochromes (Jiang et al. 1999; Kyndt et al. 2004). Understanding of light transduction in PYP requires structural information in atomic detail. A 1.4 Å crystallographic structure was determined in 1995 by Borgstahl et al. and in 1998 Düx and coworkers revealed the solution structure and backbone dynamics of PYP by NMR spectroscopy. The reaction center of PYP is protected from solvent by R52, which is believed to function as a gateway in the photocycle (Borgstahl et al. 1995; Genick et al. 1997). The chromophore, para-coumaric acid (pCA), is covalenty bound to C69 with a thioester bond and pCA participates in two short hydrogen bonds with E46 and Y42 to stabilize the negative charge of pCA in the electronic ground state, pG. Upon blue-light capture, the chromophore undergoes transcis isomerisation and the intermediate pR is formed, which subsequently relaxes to the proposed signaling state, pB. In the latter state, the reaction center is exposed and the two short hydrogen bonds are broken (Borgstahl et al. 1995; Sigala et al. 2009; Yamaguchi et al. 2009). In this paper, we present the nearly complete assignment of the backbone and side chain resonances of the pG state of PYP. Methods and experiments Uniformly 13 C, 15 N-labeled wild type PYP was overexpressed and purified as described previously (Düx et al.

Biophysical Journal, 2012

Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activ... more Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activity of its flagellar motor and thereby evade potentially harmful UV radiation. The 14 kDa soluble cytosolic photoactive yellow protein (PYP) is believed to be the primary mediator of this photophobic response, and yields a UV/Vis absorption spectrum that closely matches the bacterium's motility spectrum. In the electronic ground state, the para-coumaric acid (pCA) chromophore of PYP is negatively charged and forms two short hydrogen bonds to the side chains of Glu-46 and Tyr-42. The resulting acid triad is central to the marked pH dependence of the optical-absorption relaxation kinetics of PYP. Here, we describe an NMR approach to sequence-specifically follow all tyrosine side-chain protonation states in PYP from pH 3.41 to 11.24. The indirect observation of the nonprotonated 13 C g resonances in sensitive and well-resolved two-dimensional 13 C-1 H spectra proved to be pivotal in this effort, as observation of other ring-system resonances was hampered by spectral congestion and line-broadening due to ring flips. We observe three classes of tyrosine residues in PYP that exhibit very different pK a values depending on whether the phenolic side chain is solvent-exposed, buried, or hydrogen-bonded. In particular, our data show that Tyr-42 remains fully protonated in the pH range of 3.41-11.24, and that pH-induced changes observed in the photocycle kinetics of PYP cannot be caused by changes in the charge state of Tyr-42. It is therefore very unlikely that the pCA chromophore undergoes changes in its electrostatic interactions in the electronic ground state.

Biomacromolecules, 2022

The tiny spider makes dragline silk fibers with unbeatable toughness, all under the most innocuou... more The tiny spider makes dragline silk fibers with unbeatable toughness, all under the most innocuous conditions. Scientists have persistently tried to emulate its natural silk spinning process using recombinant proteins with a view toward creating a new wave of smart materials, yet most efforts have fallen short of attaining the native fiber's excellent mechanical properties. One reason for these shortcomings may be that artificial spider silk systems tend to be overly simplified and may not sufficiently take into account the true complexity of the underlying protein sequences and of the multidimensional aspects of the natural self-assembly process that give rise to the hierarchically structured fibers. Here, we discuss recent findings regarding the material constituents of spider dragline silk, including novel spidroin subtypes, nonspidroin proteins, and possible involvement of post-translational modifications, which together suggest a complexity that transcends the two-component MaSp1/MaSp2 system. We subsequently consider insights into the spidroin domain functions, structures, and overall mechanisms for the rapid transition from disordered soluble protein into a highly organized fiber, including the possibility of viewing spider silk self-assembly through a framework relevant to biomolecular condensates. Finally, we consider the concept of "biomimetics" as it applies to artificial spider silk production with a focus on key practical aspects of design and evaluation that may hopefully inform efforts to more closely reproduce the remarkable structure and function of the native silk fiber using artificial methods.

Protein Science, 2009

Lactococcus lactis is a promising host for (membrane) protein overproduction. Here, we describe a... more Lactococcus lactis is a promising host for (membrane) protein overproduction. Here, we describe a protocol for incorporation of selenomethionine (SeMet) into proteins expressed in L. lactis. Incorporation efficiencies of SeMet in the membrane protein complex OpuA (an ABC transporter) and the soluble protein OppA, both from L. lactis, were monitored by mass spectrometry. Both proteins incorporated SeMet with high efficiencies (>90%), which greatly extends the usefulness of the expression host L. lactis for X-ray crystallography purposes. The crystal structure of ligand-free OppA was determined at 2.4 Å resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing.