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21st Century Technologies: Protein Folding AI (AlphaFold) - CityLife
May 28, 2023 - 3:40 PM - by nmrlearner
nmrlearner's Avatar 21st Century Technologies: Protein Folding AI (AlphaFold) - CityLife

21st Century Technologies: Protein Folding AI (AlphaFold) CityLife Read here
0 Replies | 32 Views
Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes
May 27, 2023 - 2:53 PM - by nmrlearner
nmrlearner's Avatar Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

Abstract

The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few ‚??significant‚?? points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to ‚??conventional‚?? compressed sensing. We exemplify the concept of ‚??difference CS‚?? with one such case‚??the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.


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0 Replies | 165 Views
The development of nuclear magnetic resonance spectroscopy as a technique for protein structure determination - American Chemical Society
May 27, 2023 - 2:53 PM - by nmrlearner
nmrlearner's Avatar The development of nuclear magnetic resonance spectroscopy as a technique for protein structure determination American Chemical Society
The development of nuclear magnetic resonance spectroscopy as a technique for protein structure determination - American Chemical Society
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0 Replies | 22 Views
Structure Determination of Membrane Proteins by Nuclear Magnetic Resonance Spectroscopy - Annual Reviews
May 27, 2023 - 2:53 PM - by nmrlearner
nmrlearner's Avatar Structure Determination of Membrane Proteins by Nuclear Magnetic Resonance Spectroscopy Annual Reviews
Structure Determination of Membrane Proteins by Nuclear Magnetic Resonance Spectroscopy - Annual Reviews
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0 Replies | 22 Views
Stability and Solubility of De Novo Proteins Compared to Computer ... - Technology Networks
May 27, 2023 - 2:53 PM - by nmrlearner
nmrlearner's Avatar Stability and Solubility of De Novo Proteins Compared to Computer ... - Technology Networks

Stability and Solubility of De Novo Proteins Compared to Computer ... Technology Networks Read here
0 Replies | 28 Views
[NMR paper] Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR
May 27, 2023 - 2:53 PM - by nmrlearner
nmrlearner's Avatar Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR

An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside living cells. We examined an RNA aptamer for HIV-1 Tat (TA), which had been found to trap Tat and repress its function in living human cells. We first used in vitro NMR to examine the interaction between TA and a part of Tat containing the binding...

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0 Replies | 28 Views
[NMR paper] NMR and Patch-Clamp Characterization of Yeast Mitochondrial Pyruvate Carrier Complexes
May 27, 2023 - 2:53 PM - by nmrlearner
nmrlearner's Avatar NMR and Patch-Clamp Characterization of Yeast Mitochondrial Pyruvate Carrier Complexes

The mitochondrial pyruvate carrier (Mpc) plays an indispensable role in the transport of pyruvates across the mitochondrial inner membrane. Despite the two distinct homologous proteins, Mpc1 and Mpc2, were identified in 2012, there are still controversies on the basic functional units and oligomeric state of Mpc complexes. In this study, yeast Mpc1 and Mpc2 proteins were expressed in a prokaryotic heterologous system. Both homo- and hetero-dimers were successfully reconstituted in mixed...

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0 Replies | 25 Views
[NMR paper] Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes
May 27, 2023 - 2:53 PM - by nmrlearner
nmrlearner's Avatar Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few "significant" points. The more compressible the spectrum, the fewer experimental NUS points needed in order for...

More...
0 Replies | 25 Views
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