Understanding the impacts of self-shuffling approach on structure and function of shuffled endoglucanase enzyme via MD simulations

AbstractObjectiveWe identify the impacts of structural differences on functionality of EG3_S2 endoglucanase enzyme with MD studies. The results of previous experimental studies have been explained in details with computational approach. The objective of this study is to explain the functional differences between shuffled enzyme (EG3_S2) and its native counterpart (EG3_nat) from Trichoderma reseei, via Molecular Dynamics approach.Materials and methodsFor this purpose, we performed MD simulations along 30 ns at three different reaction temperatures collected as NpT ensemble, and then monitored the backbone motion, flexibilities of residues, and intramolecular interactions of EG3_S2 and EG3_nat enzymes.ResultsAccording to MD results, we conclude that EG3_S2 and EG3_nat enzymes have unique RMSD patterns, e.g. RMSD pattern of EG3_S2 is more dynamic than that of EG3_nat at all temperatures. In addition to this dynamicity, EG3_S2 establishes more salt bridge interactions than EG3_nat.ConclusionBy taking these results into an account with the preservation of catalytic Glu residues in a proper manner, we explain the structural basis of differences between shuffled and native enzyme via molecular dynamic studies.

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Visualization of Head–Head Interactions in the Inhibited State of Smooth Muscle Myosin

The Journal of Cell Biology ◽

10.1083/jcb.147.7.1385 ◽

1999 ◽

Vol 147 (7) ◽

pp. 1385-1390 ◽

Cited By ~ 84

Author(s):

Thomas Wendt ◽

Dianne Taylor ◽

Terri Messier ◽

Kathleen M. Trybus ◽

Kenneth A. Taylor

Keyword(s):

Smooth Muscle ◽

Smooth Muscle Myosin ◽

Intramolecular Interactions ◽

Actin Binding ◽

Structural Basis ◽

Binding Interface ◽

Structural Differences ◽

Muscle Myosin ◽

Positively Charged ◽

Phosphoryla Tion

The structural basis for the phosphoryla- tion-dependent regulation of smooth muscle myosin ATPase activity was investigated by forming two- dimensional (2-D) crystalline arrays of expressed unphosphorylated and thiophosphorylated smooth muscle heavy meromyosin (HMM) on positively charged lipid monolayers. A comparison of averaged 2-D projections of both forms at 2.3-nm resolution reveals distinct structural differences. In the active, thiophosphorylated form, the two heads of HMM interact intermolecularly with adjacent molecules. In the unphosphorylated or inhibited state, intramolecular interactions position the actin-binding interface of one head onto the converter domain of the second head, thus providing a mechanism whereby the activity of both heads could be inhibited.

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Review for "“Seat of the soul”? The structure and function of the pineal gland in women with alleged spirit possession—Results of two experimental studies"

10.1002/brb3.1693/v2/review1 ◽

2020 ◽

Keyword(s):

Pineal Gland ◽

Spirit Possession ◽

Experimental Studies ◽

Structure And Function ◽

And Function

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Understanding the Structure and Function of the DcaP Channel from Acinetobacter baumannii using MD Simulations

Biophysical Journal ◽

10.1016/j.bpj.2017.11.2691 ◽

2018 ◽

Vol 114 (3) ◽

pp. 491a

Author(s):

Jigneshkumar D. Prajapati ◽

Satya Prathyusha Bhamidimarri ◽

Michael Zahn ◽

Dirk Bumann ◽

Mathias Winterhalter ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Md Simulations ◽

Structure And Function ◽

And Function

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Complex Analyses of Plankton Structure and Function

The Scientific World JOURNAL ◽

10.1100/tsw.2001.19 ◽

2001 ◽

Vol 1 ◽

pp. 119-132 ◽

Cited By ~ 4

Author(s):

Karl E. Havens

Keyword(s):

Size Structure ◽

Experimental Studies ◽

Structure And Function ◽

Size Spectrum ◽

Phytoplankton Productivity ◽

Resource Managers ◽

Carbon Transfer ◽

And Function ◽

Freshwater Plankton ◽

Plankton Communities

This paper critically evaluates some complex methods that have been used to characterize the structure and function of freshwater plankton communities. The focus is on methods related to plankton size structure and carbon transfer. The specific methods reviewed are 1) size spectrum analysis, 2) size-fractionated phytoplankton productivity, 3) size-fractionated zooplankton grazing, 4) plankton ecological transfer efficiency, and 5) grazer effects on phytoplankton community structure. Taken together, these methods can provide information on community ecological properties that are directly related to practical issues including water quality and fisheries productivity. However, caution is warranted since application without a complete understanding of assumptions and context of the manipulations could lead to erroneous conclusions. As an example, experimental studies involving the addition or removal of zooplankton, especially when coupled with nutrient addition treatments, could provide information on the degree of consumer vs. resource control of phytoplankton. Resource managers subsequently could use this information in developing effective measures for controlling nuisance algal biomass. However, the experiments must be done critically and with sufficient safeguards and other measurements to ensure that treatments (e.g., zooplankton exclosure by screening of water) actually are successful and do not introduce other changes in the community (e.g., removal of large algae). In all of the methods described here, the investigator must take care when generalizing results and, in particular, carry out a sufficient number of replications to encompass both the major seasonal and spatial variation that occurs in the ecosystem.

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Application of MD Simulations to Predict Membrane Properties of MOFs

Journal of Nanomaterials ◽

10.1155/2015/136867 ◽

2015 ◽

Vol 2015 ◽

pp. 1-9 ◽

Cited By ~ 13

Author(s):

Elda Adatoz ◽

Seda Keskin

Keyword(s):

Metal Organic Frameworks ◽

Experimental Studies ◽

Molecular Simulations ◽

Md Simulations ◽

Research Field ◽

Computational Approach ◽

Membrane Properties ◽

Important Research ◽

Zeolite Membranes ◽

Metal Organic

Metal organic frameworks (MOFs) are a new group of nanomaterials that have been widely examined for various chemical applications. Gas separation using MOF membranes has become an increasingly important research field in the last years. Several experimental studies have shown that thin-film MOF membranes can outperform well known polymer and zeolite membranes due to their higher gas permeances and selectivities. Given the very large number of available MOF materials, it is impractical to fabricate and test the performance of every single MOF membrane using purely experimental techniques. In this study, we used molecular simulations, Monte Carlo and Molecular Dynamics, to estimate both single-gas and mixture permeances of MOF membranes. Predictions of molecular simulations were compared with the experimental gas permeance data of MOF membranes in order to validate the accuracy of our computational approach. Results show that computational methodology that we described in this work can be used to accurately estimate membrane properties of MOFs prior to extensive experimental efforts.

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Structural Basis of Redox Signaling in Photosynthesis: Structure and Function of Ferredoxin:thioredoxin Reductase and Target Enzymes

Photosynthesis Research ◽

10.1023/b:pres.0000017194.34167.6d ◽

2004 ◽

Vol 79 (3) ◽

pp. 233-248 ◽

Cited By ~ 31

Author(s):

Shaodong Dai ◽

Kenth Johansson ◽

Myroslawa Miginiac-Maslow ◽

Peter Schürmann ◽

Hans Eklund

Keyword(s):

Redox Signaling ◽

Structure And Function ◽

Structural Basis ◽

And Function ◽

Ferredoxin:Thioredoxin Reductase

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EXPERIMENTAL STUDIES ON THE HISTOLOGIC STRUCTURE AND FUNCTION OF AQUAEDUCTUS COCHLEAE

Nippon Jibiinkoka Gakkai Kaiho ◽

10.3950/jibiinkoka.55.907 ◽

1952 ◽

Vol 55 (11) ◽

pp. 907-916

Author(s):

M. KATAGI

Keyword(s):

Experimental Studies ◽

Structure And Function ◽

And Function

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Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study

10.26434/chemrxiv.13567349 ◽

2021 ◽

Author(s):

Aashish Bhatt ◽

Md. Ehesan Ali

Keyword(s):

Hydrogen Bonding ◽

In Silico ◽

Density Functional ◽

Experimental Studies ◽

Salt Bridge ◽

Md Simulations ◽

Enzymatic Activities ◽

Wild Type ◽

Long Distance

<div>Human cystathionine β-synthase (hCBS) is a unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyses the condensation reactions in the transsulfuration pathways. The specific role of Heme in the enzymatic activities has not yet been established, however, several experimental studies indicated the bi-directional communications between the Heme and PLP. Performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme, we have investigated <i>In Silico</i> dynamical aspects of the bi-directional communications. Furthermore, we have investigated the comparative aspects of electron density overlap across the communicating pathways adopting the density functional theory (DFT) in conjunction with the hybrid exchange correlation functional for the CSB<sup>WT</sup> (wild-type) and CBS<sup>R266K</sup> (mutated) case. The atomistic dynamical simulations and subsequent explorations of the electronic structure not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control the such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns as well as salt-bridge interactions play the pivotal role in such long distant bi-directional communications.</div>

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Refinement of a Cryo-EM Structure of hERG: Bridging Structure and Function

10.1101/2020.09.11.293266 ◽

2020 ◽

Author(s):

H.M. Khan ◽

J. Guo ◽

H.J. Duff ◽

D. P. Tieleman ◽

S. Y. Noskov

Keyword(s):

Molecular Dynamics ◽

High Resolution ◽

Salt Bridge ◽

Structure And Function ◽

Channel Structure ◽

Salt Bridges ◽

Voltage Sensing ◽

Chain Conformations ◽

And Function ◽

Voltage Sensing Domain

AbstractThe human ether-a-go-go-related gene (hERG) encodes the voltage gated potassium channel (KCNH2 or Kv11.1, commonly known as hERG). This channel plays a pivotal role in the stability of phase 3 repolarization of the cardiac action potential. Although a high-resolution cryo-EM structure is available for its depolarized (open) state, the structure surprisingly did not feature many functionally important interactions established by previous biochemical and electrophysiology experiments. Using Molecular Dynamics Flexible Fitting (MDFF), we refined the structure and recovered the missing functionally relevant salt bridges in hERG in its depolarized state. We also performed electrophysiology experiments to confirm the functional relevance of a novel salt bridge predicted by our refinement protocol. Our work shows how refinement of a high-resolution cryo-EM structure helps to bridge the existing gap between the structure and function in the voltage-sensing domain (VSD) of hERG.Statement of SignificanceCryo-EM has emerged as a major breakthrough technique in structural biology of membrane proteins. However, even high-resolution Cryo-EM structures contain poor side chain conformations and interatomic clashes. A high-resolution cryo-EM structure of hERG1 has been solved in the depolarized (open) state. The state captured by Cryo-EM surprisingly did not feature many functionally important interactions established by previous experiments. Molecular Dynamics Flexible Fitting (MDFF) used to enable refinement of the hERG1 channel structure in complex membrane environment re-establishing key functional interactions in the voltage sensing domain.

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