Molecular Dynamics Approach in the Comparison of Wild-Type and Mutant Paraoxonase-1 Apoenzyme Form

Bioinformatics and Biology Insights ◽

10.4137/bbi.s25626 ◽

2015 ◽

Vol 9 ◽

pp. BBI.S25626 ◽

Cited By ~ 3

Author(s):

Khadija Amine ◽

Lamia Miri ◽

Adil Naimi ◽

Rachid Saile ◽

Abderrahmane El Kharrim ◽

...

Keyword(s):

Molecular Dynamics ◽

Active Site ◽

Paraoxonase 1 ◽

Wild Type ◽

Repetitive Movement ◽

Catalytic Core ◽

In The Wild ◽

Dynamics Simulations ◽

L1 And L2 ◽

The Impact

There is some evidence linking the mammalian paraoxonase-1 (PON1) loops (L1 and L2) to an increased flexibility and reactivity of its active site with potential substrates. The aim of this work is to study the structural, dynamical, and functional effects of the most flexible regions close to the active site and to determine the impact of mutations on the protein. For both models, wild-type (PON1wild) and PON1 mutant (PON1mut) models, the L1 loop and Q/R and L/M mutations were constructed using MODELLER software. Molecular dynamics simulations of 20 ns at 300 K on fully modeled PON1wild and PON1mut apoenzyme have been done. Detailed analyses of the root-mean-square deviation and fluctuations, H-bonding pattern, and torsion angles have been performed. The PON1wild results were then compared with those obtained for the PON1mut. Our results show that the active site in the wild-type structure is characterized by two distinct movements of opened and closed conformations of the L1 and L2 loops. The alternating and repetitive movement of loops at specific times is consistent with the presence of 11 defined hydrogen bonds. In the PON1mut, these open-closed movements are therefore totally influenced and repressed by the Q/R and L/M mutations. In fact, these mutations seem to impact the PON1mut active site by directly reducing the catalytic core flexibility, while maintaining a significant mobility of the switch regions delineated by the loops surrounding the active site. The impact of the studied mutations on structure and dynamics proprieties of the protein may subsequently contribute to the loss of both flexibility and activity of the PON1 enzyme.

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The Impact of Mutation L138F/L210F on the Orai Channel: A Molecular Dynamics Simulation Study

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.755247 ◽

2021 ◽

Vol 8 ◽

Author(s):

Xiaoqian Zhang ◽

Hua Yu ◽

Xiangdong Liu ◽

Chen Song

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Calcium Release ◽

Hydrophobic Interactions ◽

Dynamics Simulation ◽

Wild Type ◽

Hydrophobic Region ◽

In The Wild ◽

Dynamics Simulations ◽

The Impact

The calcium release-activated calcium channel, composed of the Orai channel and the STIM protein, plays a crucial role in maintaining the Ca2+ concentration in cells. Previous studies showed that the L138F mutation in the human Orai1 creates a constitutively open channel independent of STIM, causing severe myopathy, but how the L138F mutation activates Orai1 is still unclear. Here, based on the crystal structure of Drosophila melanogaster Orai (dOrai), molecular dynamics simulations for the wild-type (WT) and the L210F (corresponding to L138F in the human Orai1) mutant were conducted to investigate their structural and dynamical properties. The results showed that the L210F dOrai mutant tends to have a more hydrated hydrophobic region (V174 to F171), as well as more dilated basic region (K163 to R155) and selectivity filter (E178). Sodium ions were located deeper in the mutant than in the wild-type. Further analysis revealed two local but essential conformational changes that may be the key to the activation. A rotation of F210, a previously unobserved feature, was found to result in the opening of the K163 gate through hydrophobic interactions. At the same time, a counter-clockwise rotation of F171 occurred more frequently in the mutant, resulting in a wider hydrophobic gate with more hydration. Ultimately, the opening of the two gates may facilitate the opening of the Orai channel independent of STIM.

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Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1812204115 ◽

2018 ◽

Vol 115 (52) ◽

pp. E12192-E12200 ◽

Cited By ~ 13

Author(s):

Haoran Yu ◽

Paul A. Dalby

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Active Site ◽

Dynamic Networks ◽

Aromatic Aldehydes ◽

Active Site Residues ◽

Trade Off ◽

Highly Correlated ◽

Dynamics Simulations ◽

The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

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Origin of Conformational Dynamics in a Globular Protein

10.1101/724286 ◽

2019 ◽

Author(s):

Adam M. Damry ◽

Marc M. Mayer ◽

Aron Broom ◽

Natalie K. Goto ◽

Roberto A. Chica

Keyword(s):

Conformational Dynamics ◽

Protein Structures ◽

Vital Role ◽

Globular Protein ◽

Conformational Exchange ◽

Solution Nmr ◽

Wild Type ◽

In The Wild ◽

Dynamics Simulations ◽

The Impact

AbstractProtein structures are dynamic, undergoing specific motions that can play a vital role in function. However, the link between primary sequence and conformational dynamics remains poorly understood. Here, we studied how conformational dynamics can arise in a globular protein by evaluating the impact of individual substitutions of core residues in DANCER-3, a streptococcal protein G domain β1 (Gβ1) variant that we previously designed to undergo a specific mode of conformational exchange that has never been observed in the wild-type protein. Using a combination of solution NMR experiments and molecular dynamics simulations, we demonstrate that only two mutations are necessary to create this conformational exchange, and that these mutations work synergistically, with one destabilizing the native Gβ1 structure and the other allowing two new conformational states to be accessed on the energy landscape. Overall, our results show how conformational dynamics can appear in a stable globular fold, a critical step in the molecular evolution of new dynamics-linked functions.

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The Impact of Active Site Mutations of South African HIV PR on Drug Resistance: Insight from Molecular Dynamics Simulations, Binding Free Energy and Per-Residue Footprints

Chemical Biology & Drug Design ◽

10.1111/cbdd.12262 ◽

2014 ◽

Vol 83 (4) ◽

pp. 472-481 ◽

Cited By ~ 9

Author(s):

Shaimaa M. Ahmed ◽

Glenn E. M. Maguire ◽

Hendrik G. Kruger ◽

Thirumala Govender

Keyword(s):

Molecular Dynamics ◽

Drug Resistance ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

South African ◽

Active Site ◽

Binding Free Energy ◽

Dynamics Simulations ◽

The Impact ◽

Active Site Mutations

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Computational insights into active site shaping for substrate specificity and reaction regioselectivity in the EXTL2 retaining glycosyltransferase

Organic & Biomolecular Chemistry ◽

10.1039/c7ob01937h ◽

2017 ◽

Vol 15 (43) ◽

pp. 9095-9107 ◽

Cited By ~ 5

Author(s):

Fernanda Mendoza ◽

José M. Lluch ◽

Laura Masgrau

Keyword(s):

Molecular Dynamics ◽

Substrate Specificity ◽

Molecular Dynamics Simulations ◽

Active Site ◽

Wild Type ◽

Dynamics Simulations

QM(DFT)/MM calculations and molecular dynamics simulations on wild-type retaining α1,4-N-acetylhexosaminyltransferase (EXTL2) and Arg293Ala, Asp246Ala, Arg293Ala/Asp246Ala and Asp246Glu mutants are used to understand the role of these two residues.

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Toward the design of efficient transglycosidases: the case of the GH1 of Thermus thermophilus

Protein Engineering Design and Selection ◽

10.1093/protein/gzz032 ◽

2019 ◽

Author(s):

Benoit David ◽

Philippe Arnaud ◽

Charles Tellier ◽

Yves-Henri Sanejouand

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Glycoside Hydrolase ◽

Thermus Thermophilus ◽

Wild Type ◽

Acid Base ◽

In The Wild ◽

Dynamics Simulations

AbstractUsing the information available in the sequences of well-characterized transglycosidases found in plants, mutations were introduced in the glycoside hydrolase of the bacterium Thermus thermophilus, with the aim of turning it into an efficient transglycosidase. All mutants happen to have fair catalytic efficiencies, being at worst 25 times less efficient than the wild type. Noteworthy, W120F, one of our high transglycosylation yield (≈ 50%) mutants, is only two times less efficient than the wild type. Interestingly, while in the wild type the sidechain of the acid–base is only found able to sample a pair of equivalent conformations during 0.5-μs-long molecular dynamics simulations, its flexibility is much higher in the case of the high transglycosylation yield mutants. Our results thus suggest that engineering the flexibility of the acid–base of a retaining glycoside hydrolase could be a general way to turn it into an efficient transglycosidase.

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Substitution of a Surface-Exposed Residue Involved in an Allosteric Network Enhances Tryptophan Synthase Function in Cells

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.679915 ◽

2021 ◽

Vol 8 ◽

Author(s):

Rebecca N. D’Amico ◽

Yuliana K. Bosken ◽

Kathleen F. O’Rourke ◽

Alec M. Murray ◽

Woudasie Admasu ◽

...

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Active Site ◽

Beta Subunit ◽

Alpha Subunit ◽

Tryptophan Synthase ◽

Wild Type ◽

Auxotrophic Strain ◽

Hydrophobic Tunnel ◽

Dynamics Simulations

Networks of noncovalent amino acid interactions propagate allosteric signals throughout proteins. Tryptophan synthase (TS) is an allosterically controlled bienzyme in which the indole product of the alpha subunit (αTS) is transferred through a 25 Å hydrophobic tunnel to the active site of the beta subunit (βTS). Previous nuclear magnetic resonance and molecular dynamics simulations identified allosteric networks in αTS important for its function. We show here that substitution of a distant, surface-exposed network residue in αTS enhances tryptophan production, not by activating αTS function, but through dynamically controlling the opening of the indole channel and stimulating βTS activity. While stimulation is modest, the substitution also enhances cell growth in a tryptophan-auxotrophic strain of Escherichia coli compared to complementation with wild-type αTS, emphasizing the biological importance of the network. Surface-exposed networks provide new opportunities in allosteric drug design and protein engineering, and hint at potential information conduits through which the functions of a metabolon or even larger proteome might be coordinated and regulated.

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Exploration of the cofactor specificity of wild-type phosphite dehydrogenase and its mutant using molecular dynamics simulations

RSC Advances ◽

10.1039/d1ra00221j ◽

2021 ◽

Vol 11 (24) ◽

pp. 14527-14533

Author(s):

Kunlu Liu ◽

Min Wang ◽

Yubo Zhou ◽

Hongxiang Wang ◽

Yudong Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Wild Type ◽

Cofactor Specificity ◽

Phosphite Dehydrogenase ◽

Dynamics Simulations

Phosphite dehydrogenase (Pdh) catalyzes the NAD-dependent oxidation of phosphite to phosphate with the formation of NADH.

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Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

Biochemical Journal ◽

10.1042/bcj20180874 ◽

2019 ◽

Vol 476 (6) ◽

pp. 991-1003 ◽

Cited By ~ 1

Author(s):

Vijaykumar Pillalamarri ◽

Tarun Arya ◽

Neshatul Haque ◽

Sandeep Chowdary Bala ◽

Anil Kumar Marapaka ◽

...

Keyword(s):

Natural Product ◽

Active Site ◽

Covalent Modification ◽

Structural Basis ◽

Wild Type ◽

Methionine Aminopeptidases ◽

Synthetic Derivative ◽

Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

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