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

Papers by Nur Alia Oktaviani

Chemical Communications, 2019

The effect of ions on the structure and dynamics of a spider silk protein is elucidated. Chaotrop... more The effect of ions on the structure and dynamics of a spider silk protein is elucidated. Chaotropic ions prevent intra-and intermolecular interactions on the repetitive domain, which are required to maintain the solubility, while kosmotropic ions promote hydrogen bond interactions in the glycine-rich region, which are a prerequisite for b-sheet formation.

Biomacromolecules, Apr 4, 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.

Journal of Biomolecular NMR, Mar 28, 2015

Protein Science, May 1, 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 A ˚resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing.

Unusual pKa Values Mediate the Self-Assembly of Spider Dragline Silk Proteins

Biomacromolecules

Science Advances

Spider silks are among the toughest known materials and thus provide models for renewable, biodeg... more Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.

Chemical Shift Assignnment of Recombinant Repetitive Domain of Spider Dragline Silk

Journal of Back and Musculoskeletal Rehabilitation, 2018

Salt- and pH-dependent dimerization of N-terminal domain of spider silk protein

Biomolecular NMR Assignments, 2020

Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk... more Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk protein mainly consists of two proteins, namely, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). The MaSp N-terminal domain (NTD) conformation displays a strong dependence on ion and pH gradients, which is crucial for the self-assembly behavior of spider silk. In the spider major ampullate gland, where the pH is neutral and concentration of NaCl is high, the NTD forms a monomer. In contrast, within the spinning duct, where pH becomes more acidic (to pH ~ 5) and the concentration of salt is low, NTD forms a dimer in antiparallel orientation. In this study, we report near-complete backbone and side chain chemical shift assignment of the monomeric form of NTD of MaSp2 from Nephila clavipes at pH 7 in the presence of 300 mM NaCl. Our NMR data demonstrate that secondary structure of monomeric form of NTD MaSp2 consists of five helix regions.

Communications Biology, 2020

Photosynthetic microorganisms such as cyanobacteria, purple bacteria and microalgae have attracte... more Photosynthetic microorganisms such as cyanobacteria, purple bacteria and microalgae have attracted great interest as promising platforms for economical and sustainable production of bioenergy, biochemicals, and biopolymers. Here, we demonstrate heterotrophic production of spider dragline silk proteins, major ampullate spidroins (MaSp), in a marine photosynthetic purple bacterium, Rhodovulum sulfidophilum, under both photoheterotrophic and photoautotrophic growth conditions. Spider silk is a biodegradable and biocompatible material with remarkable mechanical properties. R. sulfidophilum grow by utilizing abundant and renewable nonfood bioresources such as seawater, sunlight, and gaseous CO2 and N2, thus making this photosynthetic microbial cell factory a promising green and sustainable production platform for proteins and biopolymers, including spider silks.

Nature communications, May 29, 2018

The β-sheet is the key structure underlying the excellent mechanical properties of spider silk. H... more The β-sheet is the key structure underlying the excellent mechanical properties of spider silk. However, the comprehensive mechanism underlying β-sheet formation from soluble silk proteins during the transition into insoluble stable fibers has not been elucidated. Notably, the assembly of repetitive domains that dominate the length of the protein chains and structural features within the spun fibers has not been clarified. Here we determine the conformation and dynamics of the soluble precursor of the repetitive domain of spider silk using solution-state NMR, far-UV circular dichroism and vibrational circular dichroism. The soluble repetitive domain contains two major populations: ~65% random coil and ~24% polyproline type II helix (PPII helix). The PPII helix conformation in the glycine-rich region is proposed as a soluble prefibrillar region that subsequently undergoes intramolecular interactions. These findings unravel the mechanism underlying the initial step of β-sheet formatio...

Angewandte Chemie, Nov 29, 2016

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.

Unraveling electrostatic interactions in the active site of photoactive yellow proteins

FEBS Journal, 2012

Backbone 1H, 13C,and 15N chemical shift assignments for alpha-synuclein at different pH and temperature

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.

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide

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.

Chemical Communications, 2019

The effect of ions on the structure and dynamics of a spider silk protein is elucidated. Chaotrop... more The effect of ions on the structure and dynamics of a spider silk protein is elucidated. Chaotropic ions prevent intra-and intermolecular interactions on the repetitive domain, which are required to maintain the solubility, while kosmotropic ions promote hydrogen bond interactions in the glycine-rich region, which are a prerequisite for b-sheet formation.

Biomacromolecules, Apr 4, 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.

Journal of Biomolecular NMR, Mar 28, 2015

Protein Science, May 1, 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 A ˚resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing.

Unusual pKa Values Mediate the Self-Assembly of Spider Dragline Silk Proteins

Biomacromolecules

Science Advances

Spider silks are among the toughest known materials and thus provide models for renewable, biodeg... more Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.

Chemical Shift Assignnment of Recombinant Repetitive Domain of Spider Dragline Silk

Journal of Back and Musculoskeletal Rehabilitation, 2018

Salt- and pH-dependent dimerization of N-terminal domain of spider silk protein

Biomolecular NMR Assignments, 2020

Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk... more Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk protein mainly consists of two proteins, namely, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). The MaSp N-terminal domain (NTD) conformation displays a strong dependence on ion and pH gradients, which is crucial for the self-assembly behavior of spider silk. In the spider major ampullate gland, where the pH is neutral and concentration of NaCl is high, the NTD forms a monomer. In contrast, within the spinning duct, where pH becomes more acidic (to pH ~ 5) and the concentration of salt is low, NTD forms a dimer in antiparallel orientation. In this study, we report near-complete backbone and side chain chemical shift assignment of the monomeric form of NTD of MaSp2 from Nephila clavipes at pH 7 in the presence of 300 mM NaCl. Our NMR data demonstrate that secondary structure of monomeric form of NTD MaSp2 consists of five helix regions.

Communications Biology, 2020

Photosynthetic microorganisms such as cyanobacteria, purple bacteria and microalgae have attracte... more Photosynthetic microorganisms such as cyanobacteria, purple bacteria and microalgae have attracted great interest as promising platforms for economical and sustainable production of bioenergy, biochemicals, and biopolymers. Here, we demonstrate heterotrophic production of spider dragline silk proteins, major ampullate spidroins (MaSp), in a marine photosynthetic purple bacterium, Rhodovulum sulfidophilum, under both photoheterotrophic and photoautotrophic growth conditions. Spider silk is a biodegradable and biocompatible material with remarkable mechanical properties. R. sulfidophilum grow by utilizing abundant and renewable nonfood bioresources such as seawater, sunlight, and gaseous CO2 and N2, thus making this photosynthetic microbial cell factory a promising green and sustainable production platform for proteins and biopolymers, including spider silks.

Nature communications, May 29, 2018

The β-sheet is the key structure underlying the excellent mechanical properties of spider silk. H... more The β-sheet is the key structure underlying the excellent mechanical properties of spider silk. However, the comprehensive mechanism underlying β-sheet formation from soluble silk proteins during the transition into insoluble stable fibers has not been elucidated. Notably, the assembly of repetitive domains that dominate the length of the protein chains and structural features within the spun fibers has not been clarified. Here we determine the conformation and dynamics of the soluble precursor of the repetitive domain of spider silk using solution-state NMR, far-UV circular dichroism and vibrational circular dichroism. The soluble repetitive domain contains two major populations: ~65% random coil and ~24% polyproline type II helix (PPII helix). The PPII helix conformation in the glycine-rich region is proposed as a soluble prefibrillar region that subsequently undergoes intramolecular interactions. These findings unravel the mechanism underlying the initial step of β-sheet formatio...

Angewandte Chemie, Nov 29, 2016

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.

Unraveling electrostatic interactions in the active site of photoactive yellow proteins

FEBS Journal, 2012

Backbone 1H, 13C,and 15N chemical shift assignments for alpha-synuclein at different pH and temperature

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.

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide

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.