scholarly journals Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

2014 ◽  
Vol 119 (3) ◽  
pp. 861-872 ◽  
Author(s):  
M. Olivia Kim ◽  
Patrick G. Blachly ◽  
Joseph W. Kaus ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Free Energies ◽  
Constant Ph ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics ◽  
Binding Free Energies

scholarly journals Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 334
Author(s):  
Shih-Ting Hong ◽  
Yu-Cheng Su ◽  
Yu-Jen Wang ◽  
Tian-Lu Cheng ◽  
Yeng-Tseng Wang
Keyword(s):  
Molecular Dynamics ◽  
Tnf Alpha ◽  
Complex Structures ◽  
Binding Characteristics ◽  
Accelerated Molecular Dynamics ◽  
Constant Ph ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics ◽  
Antibody Drug

Humira is a monoclonal antibody that binds to TNF alpha, inactivates TNF alpha receptors, and inhibits inflammation. Neonatal Fc receptors can mediate the transcytosis of Humira–TNF alpha complex structures and process them toward degradation pathways, which reduces the therapeutic effect of Humira. Allowing the Humira–TNF alpha complex structures to dissociate to Humira and soluble TNF alpha in the early endosome to enable Humira recycling is crucial. We used the cytoplasmic pH (7.4), the early endosomal pH (6.0), and pKa of histidine side chains (6.0–6.4) to mutate the residues of complementarity-determining regions with histidine. Our engineered Humira (W1-Humira) can bind to TNF alpha in plasma at neutral pH and dissociate from the TNF alpha in the endosome at acidic pH. We used the constant-pH molecular dynamics, Gaussian accelerated molecular dynamics, two-dimensional potential mean force profiles, and in vitro methods to investigate the characteristics of W1-Humira. Our results revealed that the proposed Humira can bind TNF alpha with pH-dependent affinity in vitro. The W1-Humira was weaker than wild-type Humira at neutral pH in vitro, and our prediction results were close to the in vitro results. Furthermore, our approach displayed a high accuracy in antibody pH-dependent binding characteristics prediction, which may facilitate antibody drug design. Advancements in computational methods and computing power may further aid in addressing the challenges in antibody drug design.

scholarly journals pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL

2018 ◽  
Vol 20 (5) ◽  
pp. 3523-3530 ◽  
Author(s):  
Zhi Yue ◽  
Jana Shen
Keyword(s):  
Molecular Dynamics ◽  
Energy Barrier ◽  
Molten Globule ◽  
Free Energy Barrier ◽  
Molten Globule State ◽  
Constant Ph ◽  
Ph Dependent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics ◽  
Folding Free Energy

Constant pH molecular dynamics simulations of BBL reveals negligible folding free energy barrier that is pH dependent and a sparsely populated dry molten globule state.

scholarly journals The pH-Dependent Conformational States of Kyotorphin: A Constant-pH Molecular Dynamics Study

2007 ◽  
Vol 92 (6) ◽  
pp. 1836-1845 ◽  
Author(s):  
Miguel Machuqueiro ◽  
António M. Baptista
Keyword(s):  
Molecular Dynamics ◽  
Conformational States ◽  
Constant Ph ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics

scholarly journals pH-Dependent Cooperativity and Existence of a Dry Molten Globule in the Folding of a Miniprotein BBL

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue
Keyword(s):  
Molecular Dynamics ◽  
Protein Dynamics ◽  
Molten Globule ◽  
Hydrophobic Core ◽  
Solution Ph ◽  
Downhill Folding ◽  
Constant Ph ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics ◽  
Dynamics Stability

<p>Solution pH plays an important role in protein dynamics, stability, and folding; however, detailed mechanisms remain poorly understood. Here we use continuous constant pH molecular dynamics in explicit solvent with pH replica exchange to explore the pH-dependent stability and folding mechanism of a miniprotein BBL, which has drawn intense debate in the past. Consistent with the two-state model, simulations showed native and denatured states with pH-dependent populations. However, at pH 7, the folding barrier is marginal and it vanishes as pH is decreased to 5, in agreement with the downhill folding hypothesis. As pH continues to decrease, the unfolding barrier lowers and denaturation is triggered by the protonation of Asp162, consistent with experimental evidence. Interestingly, unfolding proceeded via a sparsely populated intermediate, with intact secondary structure and a compact, unlocked hydrophobic core shielded from solvent, lending support to the recent hypothesis of a universal dry molten globule in protein folding. Our work demonstrates that constant pH molecular dynamics is a unique tool for testing this and other hypotheses to advance the knowledge in protein dynamics, stability, and folding.</p>

scholarly journals Human IgG1 Fc pH-dependent optimization from a constant pH molecular dynamics simulation analysis

RSC Advances ◽  
2020 ◽  
Vol 10 (22) ◽  
pp. 13066-13075
Author(s):  
Yee Ying Lim ◽  
Theam Soon Lim ◽  
Yee Siew Choong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
In Silico ◽  
Simulation Analysis ◽  
Dynamics Simulation ◽  
Constant Ph ◽  
Human Igg1 ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics

An in silico IgG-Fc variant with better affinity at pH 6.0 but retained the dissociation at pH 7.5 was designed.

scholarly journals pH-Dependent Cooperativity and Existence of a Dry Molten Globule in the Folding of a Miniprotein BBL

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue
Keyword(s):  
Molecular Dynamics ◽  
Protein Dynamics ◽  
Molten Globule ◽  
Hydrophobic Core ◽  
Solution Ph ◽  
Downhill Folding ◽  
Constant Ph ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics ◽  
Dynamics Stability

<p>Solution pH plays an important role in protein dynamics, stability, and folding; however, detailed mechanisms remain poorly understood. Here we use continuous constant pH molecular dynamics in explicit solvent with pH replica exchange to explore the pH-dependent stability and folding mechanism of a miniprotein BBL, which has drawn intense debate in the past. Consistent with the two-state model, simulations showed native and denatured states with pH-dependent populations. However, at pH 7, the folding barrier is marginal and it vanishes as pH is decreased to 5, in agreement with the downhill folding hypothesis. As pH continues to decrease, the unfolding barrier lowers and denaturation is triggered by the protonation of Asp162, consistent with experimental evidence. Interestingly, unfolding proceeded via a sparsely populated intermediate, with intact secondary structure and a compact, unlocked hydrophobic core shielded from solvent, lending support to the recent hypothesis of a universal dry molten globule in protein folding. Our work demonstrates that constant pH molecular dynamics is a unique tool for testing this and other hypotheses to advance the knowledge in protein dynamics, stability, and folding.</p>

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

scholarly journals Recent development and application of constant pH molecular dynamics

2014 ◽  
Vol 40 (10-11) ◽  
pp. 830-838 ◽  
Author(s):  
Wei Chen ◽  
Brian H. Morrow ◽  
Chuanyin Shi ◽  
Jana K. Shen
Keyword(s):  
Molecular Dynamics ◽  
Constant Ph ◽  
Constant Ph Molecular Dynamics
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