The biological functions of low-frequency vibrations (phonons)

Chou, Kuo‐Chen; Kiang, Yuan-Sun

doi:10.1016/0301-4622(85)80045-4

Cited by 64 publications

(57 citation statements)

References 31 publications

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“…This might be the result of a compromise between the following two factors. On one hand, according to the "rack mechanism" [179], the active site of HIV protease can be likened to a "rack" during the peptide cleaving process. Thus, it appears that the more residues that are bound to the rack of enzyme, the more strained the peptide, and hence the more efficient the cleavage process.…”

Section: Hivcleavementioning

confidence: 99%

REVIEW : Recent advances in developing web-servers for predicting protein attributes

Chou¹,

Shen²

2009

Self Cite

277

173

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Recent advance in large-scale genome sequencing has generated a huge volume of protein sequences. In order to timely utilize the information hidden in these newly discovered sequences, it is highly desired to develop computational methods for efficiently identifying their various attributes because the information thus obtained will be very useful for both basic research and drug development. Particularly, it would be even more useful and welcome if a user-friendly web-server could be provided for each of these methods. In this minireview, a systematic introduction is presented to highlight the development of these web-servers by our group during the last three years.

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Section: Hivcleavementioning

confidence: 99%

REVIEW : Recent advances in developing web-servers for predicting protein attributes

Chou¹,

Shen²

2009

Self Cite

277

173

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“…Dr. Chou reported this mechanism in order to solve a perplexing "free-energy deficit" problem [45], which was encountered in studying the binding interaction between insulin and the insulin receptor [46]. According to the inference elaborated in [45], the wave numbers of the low-frequency phonons were in the range of , corresponding to the range of terahertz frequency ( to Hz). In the mean time, the possible biological functions of low-frequency phonons in proteins were also discussed [45].…”

Section: Basic Mechanisms Underlying the Efficacy Of Elf-emf Treatmentsmentioning

confidence: 99%

“…According to the inference elaborated in [45], the wave numbers of the low-frequency phonons were in the range of , corresponding to the range of terahertz frequency ( to Hz). In the mean time, the possible biological functions of low-frequency phonons in proteins were also discussed [45]. Subsequently, low-frequency modes have been indeed observed by Raman spectroscopy for a number of protein molecules [47,48] and different types of DNA [49][50][51][52].…”

Section: Basic Mechanisms Underlying the Efficacy Of Elf-emf Treatmentsmentioning

confidence: 99%

“…The most interesting fact is that many marvelous biological functions and their profound dynamic mechanisms, such as cooperative effects [60,63], allosteric transition [64,65], and intercalation of drugs into DNA [66,67], can be revealed through the low-frequency collective motion or resonance in protein and DNA molecules. In this regard, some phenomenological theories [57,65,67,68] were established.…”

Section: Basic Mechanisms Underlying the Efficacy Of Elf-emf Treatmentsmentioning

confidence: 99%

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Steps to the clinic with ELF EMF

Madkan¹,

Blank²,

Elson³

et al. 2009

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There have been many models to identify and analyze low-frequency motions in protein and DNA molecules. It has been successfully used to simulate various low-frequency collective motions in protein and DNA molecules. Lowfrequency motions in biomacromolecules originate from two common and intrinsic characteristics; i.e., they contain 1) a series of weak bonds, such as hydrogen bonds, and 2) a substantial mass distributed over the region of these weak bonds. Many biological functions and dynamic mechanisms, including cooperative effects have been reported. In this regard, some phenomenological theories were established. However, differences in experimental outcomes are expected since many factors could influence the outcome of experiments in EMF research. Any effect of EMF has to depend on the energy absorbed by a biological organism and on how the energy is delivered in space and time. Frequency, intensity, exposure duration, and the number of exposure episodes can affect the response, and these factors can interact with each other to produce different effects. In addition, in order to understand the biological consequence of EMF exposure, one must know whether the effect is cumulative, whether compensatory responses result, and when homeostasis will break down. Such findings will have great potential for use in translation medicine at the clinical level without being invasive.

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“…Many marvelous biological functions in proteins and DNA and their profound dynamic mechanisms, such as switch between active and inactive states [47]cooperative effects [48], allosteric transition [49], intercalation of drugs into DNA [50], and assembly of microtubules [51], can be revealed by studying their low-frequency internal motions [52] as summarized in a comprehensive review [53]. Likewise, to really understand the action mechanism of receptorligand binding or protein-drug interaction we should consider not only the static structures concerned but also the dynamical information obtained by simulating their internal motions or dynamic process.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Molecular Recognition of Human Angiotensin-Coverting Enzyme I (hACE I) and Different Inhibitors

Chu¹,

Min²,

Zhang³

et al. 2013

CTMC

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Abstract:The human angiontensin-converting enzyme I (hACEI) is a zinc metalloproteinase that hydrolytically cleaves a C-terminal dipeptide from a wide range of peptide substrates, and it plays an important role in regulating blood pressure. MD simulations and interaction energy calculations for docking and crystal structures were performed to investigate the correct conformation of the ACE with enalaprilat and nanopepetide. The analysis of root-mean-squrared fluctuation (RMSF), which is usually applied to measure the mobility and flexibility of the proteins, and dynamic correlation of residues show that the fluctuation pattern of the each two structure of the same ligand is almost the same mode. Hydrogen bond analysis shows that the correct crystal conformation is more stable than a wrong docking conformation. In addition, we are demonstrating that calculating interaction energy between protein and its ligands is an accurate and efficient way to select the correct conformation from docking conformations.

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The biological functions of low-frequency vibrations (phonons)

Cited by 64 publications

References 31 publications

REVIEW : Recent advances in developing web-servers for predicting protein attributes

REVIEW : Recent advances in developing web-servers for predicting protein attributes

Steps to the clinic with ELF EMF

Molecular Recognition of Human Angiotensin-Coverting Enzyme I (hACE I) and Different Inhibitors

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