Molecular dynamics simulation of the interaction of HLL peptide and 2D materials with individual residue resolution

Stroud, Andrew; Leuty, Gary; Muratore, Chris; Derosa, Pedro A.; Berry, Rajiv

doi:10.1016/j.commatsci.2019.109112

Cited by 4 publications

(2 citation statements)

References 48 publications

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“…There are no studies of molybdenum-peptide systems by NMR, however there are studies on molybdenumpeptide systems in general, to which NMR could feasibly be applied. Briefly, these include known molybdenum-peptide complexes such as those in Noni juice, which is used medicinally [135]; an antimicrobial assembly comprising molybdenum-polyoxometalate and a positively charged peptide [136]; MoS 2 -bound peptide complexes have been studied [137], including materials that disrupt the structure of amyloid fibrils [138] and are used as electrochemical sensors [139], e.g., as potential anticancer and antibacterial agents [140][141][142]. Furthermore, tungsten is becoming more common in our environment and may inhibit molybdoenzymes through exchange with the bound molybdenum ion in the cofactor [143], making this an increasingly relevant system to study.…”

Section: Molybdenummentioning

confidence: 99%

Studying Peptide-Metal Ion Complex Structures by Solution-State NMR

Shalev

2022

IJMS

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Metal chelation can provide structural stability and form reactive centers in metalloproteins. Approximately one third of known protein structures are metalloproteins, and metal binding, or the lack thereof, is often implicated in disease, making it necessary to be able to study these systems in detail. Peptide-metal complexes are both present in nature and can provide a means to focus on the binding region of a protein and control experimental variables to a high degree. Structural studies of peptide complexes with metal ions by nuclear magnetic resonance (NMR) were surveyed for all the essential metal complexes and many non-essential metal complexes. The various methods used to study each metal ion are presented together with examples of recent research. Many of these metal systems have been individually reviewed and this current overview of NMR studies of metallopeptide complexes aims to provide a basis for inspiration from structural studies and methodology applied in the field.

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Section: Molybdenummentioning

confidence: 99%

Studying Peptide-Metal Ion Complex Structures by Solution-State NMR

Shalev

2022

IJMS

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“…Thereby, the theoretical works of molecular modeling reported in the literature are usually done using small molecules [158]. Stroud et al [159], for instance, reported on an MD simulation to investigate the interaction between a model peptide sequence and different potential LDM candidates as transducer/substrate in biosensors platforms. That kind of simulation can also be used to study phenomena like the EDL formation, calculate free energies, etc.…”

Section: Theory and Simulation Of Biosensingmentioning

confidence: 99%

Addressing the Theoretical and Experimental Aspects of Low-Dimensional-Materials-Based FET Immunosensors: A Review

et al. 2021

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Electrochemical immunosensors (EI) have been widely investigated in the last several years. Among them, immunosensors based on low-dimensional materials (LDM) stand out, as they could provide a substantial gain in fabricating point-of-care devices, paving the way for fast, precise, and sensitive diagnosis of numerous severe illnesses. The high surface area available in LDMs makes it possible to immobilize a high density of bioreceptors, improving the sensitivity in biorecognition events between antibodies and antigens. If on the one hand, many works present promising results in using LDMs as a sensing material in EIs, on the other hand, very few of them discuss the fundamental interactions involved at the interfaces. Understanding the fundamental Chemistry and Physics of the interactions between the surface of LDMs and the bioreceptors, and how the operating conditions and biorecognition events affect those interactions, is vital when proposing new devices. Here, we present a review of recent works on EIs, focusing on devices that use LDMs (1D and 2D) as the sensing substrate. To do so, we highlight both experimental and theoretical aspects, bringing to light the fundamental aspects of the main interactions occurring at the interfaces and the operating mechanisms in which the detections are based.

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Beyond point of care diagnostics: Low-dimensional nanomaterials for electronic virus sensing

Muratore

2020

Journal of Vacuum Science &Amp; Technology A: Vacuum, Surfaces, and Films

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Influenza results in tens of thousands of deaths annually in the USA and hundreds of thousands worldwide. COVID-19, caused by the SARS-Cov-2 virus, is even more devastating in terms of patient mortality. At the time of this writing, the nanoscopic SARS-Cov-2 virus has paralyzed the world economy and resulted in what are likely permanent changes in our expectations of society and daily life. New technology is needed to reduce the economic and social impacts of diseases such as COVID-19 and prevent additional negative consequences resulting from subsequent pandemics. As viruses such as Influenza A and SARS-Cov-2 are transmitted from person to person by exposure to infected secretions, inexpensive at-home or workplace tests for the analysis of the virus content within those secretions, such as saliva or mucus from the nasopharynx (as in a swab-based test) or oropharynx (as in a saliva-based test), will be critical for a safe return to work, school, and cultural activities. The most reliable approaches for viral sensing are polymerase chain reaction and protein detection via enzyme-linked immunosorbent assay; however, these approaches require extensive sample handling, laboratory infrastructure, and long sample-to-result time. Advances are leading to increased point-of-care capability for these testing methods, but even this effort is insufficient for curbing the impact of the current pandemic. There are many options for alternative virus (or antigen) detection currently in development. These novel approaches are more amenable for testing in home or workplace without specialized equipment and training and include measurements of mass changes, heat of adsorption, electrochemical changes, changes in optical properties, and changes in electronic properties. Of these transduction mechanisms, electronic property measurements of materials as they interact with virus-containing secretions offer the greatest potential for simplicity, selectivity, and sensitivity needed to revolutionize traditional laboratory assays for at-home pathogen detection. We have, therefore, focused this review on the operation and architecture of electronic antigen sensors, specifically those demonstrating a change in electrical conductivity when interacting with a specific antigen, with hopes that a brief summary of over five decades of research in this area will be beneficial to those developing alternative, user-friendly routes for detection of viruses at this or any time. A key element in electronic virus sensing with useful sensitivity is the use of nanomaterials with ultrahigh surface-to-volume ratios, maximizing the change in charge carrier density upon adsorption events. So-called “low-dimensional materials” are materials characterized by nanoscopic length scales in at least one dimension. One-dimensional nanomaterials such as nanowires and nanotubes are well-established as effective sensing materials with potential for high sensitivity; however, their realization on a large scale has been challenging. Two-dimensional materials are planar materials with thicknesses of one or a few molecular layers and represent the ultimate limit of the surface-to-volume ratio with promising demonstrations of large-scale production and sensitive, selective virus sensing with many options for functionalization. All aspects of 2D sensor fabrication, functionalization, and use are addressed.

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Molecular dynamics simulation of the interaction of HLL peptide and 2D materials with individual residue resolution

Cited by 4 publications

References 48 publications

Studying Peptide-Metal Ion Complex Structures by Solution-State NMR

Studying Peptide-Metal Ion Complex Structures by Solution-State NMR

Addressing the Theoretical and Experimental Aspects of Low-Dimensional-Materials-Based FET Immunosensors: A Review

Beyond point of care diagnostics: Low-dimensional nanomaterials for electronic virus sensing

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