Multilayer Model of Gold Nanoparticles (AuNPs) and Its Application in the Classical Molecular Dynamics Simulation of Citrate-Capped AuNPs

Janitra, Regaputra S.; Destiarani, Wanda; Hardianto, Ari; Baroroh, Umi; Rohmatulloh, Fauzian Giansyah; Rustaman, None; Subroto, Toto; Rukiah,; Yusuf, Muhammad

doi:10.1021/acs.jpcb.3c00771

Cited by 3 publications

(1 citation statement)

References 50 publications

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“…Konvergensi energi minimum dilakukan untuk mengetahui apakah minimisasi sebelumnya sudah mencapai lokal minima. Jika belum tercapai, dilakukan penambahan pada step minimisasi sebelumnya [46]. Tahanan gaya yang digunakan sebesar 10 kkal.mol -1 .Å -2 .…”

Section: Simulasi Dinamika Molekul (Md)unclassified

Analisis Interaksi ?-Amilase Bacillus licheniformis (BLA) dan Mutannya (MTBLA) dengan Maltoheptaosa pada Suhu Tinggi menggunakan Metode In Silico

Azzahra,

Janitra,

Widayat

et al. 2023

J. Sains Kes.

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?-Amylase is an enzyme that hydrolyzes starch into oligosaccharides used in the food and health industry sector. Hydrolysis products such as maltopentose can be a high-nutrition source for patients with kidney failure and calorie deficit. Therefore, increasing the thermostability of enzymes needs to be done to meet industrial criteria. In this study, we studied the effect of the Bacillus licheniformis ?-amylase (BLA) mutation on its activity at 298 and 373 K in silico through enzyme-substrate interaction analysis. Maltoheptaose was used as a model substrate. At 373 K, the Asn190Phe mutation plays a direct role in forming interactions with the substrate while the Gln264Ser mutation does not play a direct role. At 298 K the Asn265Tyr mutation plays a direct role in the enzyme-substrate interaction. In this study, we found a relationship between enzyme-substrate interaction and activity, the most determining factor being the interaction with the catalytic residue. At 298 K, the total interaction of the mutant BLA (MTBLA)-maltoheptaose was slightly stronger than that of BLA-maltoheptaose. However, the interaction of maltoheptaose with catalytic residues in BLA is stronger than in MTBLA. This is in agreement with the previous experiment at 298 K. A similar pattern is found at 373 K. Thereby, MTBLA activity at 373 K is also not more improved than BLA. Keywords: ?-Amylase, activity, thermostability, Bacillus licheniformis, In silico Abstrak ?-Amilase merupakan enzim yang menghidrolisis pati menjadi oligosakarida yang digunakan di sektor industri makanan dan kesehatan. Produk hidrolisis seperti maltopentosa dapat menjadi sumber makanan tinggi nutrisi untuk pasien gagal ginjal dan defisit kalori. Oleh sebab itu, peningkatan termostabilitas enzim perlu dilakukan untuk memenuhi kriteria industri. Pada penelitian ini kami mempelajari pengaruh mutasi ?-amilase Bacillus licheniformis (BLA) terhadap aktivitasnya pada suhu 298 dan 373 K secara in silico melalui analisis interaksi enzim-substrat. Maltoheptaosa digunakan sebagai model substrat. Pada suhu 373 K, mutasi Asn190Phe berperan langsung membentuk interaksi dengan substrat sedangkan mutasi Gln264Ser tidak berperan langsung. Pada suhu 298 K mutasi Asn265Tyr berperan langsung terhadap interaksi enzim-substrat. Pada penelitian ini, kami menemukan hubungan antara interaksi enzim-substrat terhadap aktivitas, faktor yang paling menentukan adalah interaksinya dengan residu katalitik. Pada suhu 298 K, total interaksi mutan BLA (MTBLA)-maltoheptaosa sedikit lebih kuat dibandingkan BLA-maltoheptaosa. Namun, interaksi maltoheptaosa dengan residu katalitik pada BLA lebih kuat daripada MTBLA. Hal ini bersesuaian dengan eksperimen sebelumnya pada suhu 298 K. Pola yang mirip terlihat pada 373 K, sehingga aktivitas MTBLA pada suhu 373 K juga tidak lebih baik daripada BLA. Kata Kunci: ?-Amilase, aktivitas, termostabilitas, Bacillus licheniformis, In silico

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Section: Simulasi Dinamika Molekul (Md)unclassified

Analisis Interaksi ?-Amilase Bacillus licheniformis (BLA) dan Mutannya (MTBLA) dengan Maltoheptaosa pada Suhu Tinggi menggunakan Metode In Silico

Azzahra,

Janitra,

Widayat

et al. 2023

J. Sains Kes.

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Dynamic Metal Exchange in Nanoclusters: Isotope Labeling Sheds Light on Cellular‐like Fusion Processes

Tang,

Wang,

Han

et al. 2024

Eur J Inorg Chem

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Grasping the behavior of metal nanoclusters in solution at the atomic level is a pinnacle challenge in nanoscience. In addressing this, our work utilizes the Ag13@Ag16(BDT)12(TPP)4 (Ag29) nanocluster (where BDT represents 1,3‐benzenedithiol, and TPP is triphenylphosphine) as a template. We employ isotopic layering labeling, such as a109 Ag13@107 Ag16 core ‐shell structure, to mark the clusters. Subsequently, we conduct reactions with clusters featuring two different layering structures. Finally, we employ isotopic labeling to replace Ag in the shell, followed by analysis using ESI‐MS, enabling us to discern the process of intercluster reactions. We observed that the reactions primarily involve metal exchanges between the cores of different clusters and separately between their shells, highlighting distinct patterns of atomic‐level exchanges within these structures. This study thus offers pivotal insights into the molecular‐level mechanisms of metal exchange between clusters, significantly contributing to the development of metal nanocluster design and synthesis.

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Conformational structure of polyampholytes on the surface of a spherical metal nanoparticle under simultaneous exposure to static and alternating electric fields

Kruchinin

2024

CPM

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The simultaneous effect of external static and alternating electric fields on the composite nanosystem "gold spherical nanoparticle-polyampholyte" was studied. Radial and angular dependences of the polymer density were constructed, including in a narrow surface layer of the nanoparticle. In the case where the amplitude of the alternating dipole moment of the nanoparticle significantly exceeded the value of the static dipole moment, a ring-shaped fringe was formed in the equatorial region of the spherical gold nanoparticle. With an increase in the amplitude of the alternating electric field, the shape of the polyampholyte fringe changed from elongated in the direction of static polarization to swollen in the equatorial region of the nanoparticle. Oppositely charged links were located on those halves of the spherical nanoparticle relative to the equator, where opposite charges were induced due to the effect of the static electric field.

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Multilayer Model of Gold Nanoparticles (AuNPs) and Its Application in the Classical Molecular Dynamics Simulation of Citrate-Capped AuNPs

Cited by 3 publications

References 50 publications

Analisis Interaksi ?-Amilase Bacillus licheniformis (BLA) dan Mutannya (MTBLA) dengan Maltoheptaosa pada Suhu Tinggi menggunakan Metode In Silico

Analisis Interaksi ?-Amilase Bacillus licheniformis (BLA) dan Mutannya (MTBLA) dengan Maltoheptaosa pada Suhu Tinggi menggunakan Metode In Silico

Dynamic Metal Exchange in Nanoclusters: Isotope Labeling Sheds Light on Cellular‐like Fusion Processes

Conformational structure of polyampholytes on the surface of a spherical metal nanoparticle under simultaneous exposure to static and alternating electric fields

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