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Article ; Online: Classification of GTP-dependent K-Ras4B active and inactive conformational states.

Narayan, Brajesh / Kiel, Christina / Buchete, Nicolae-Viorel

2023 Volume 158, Issue 9, Page(s) 91104

Abstract: Classifying reliably active and inactive molecular conformations of wildtype (WT) and mutated oncogenic proteins is a key, ongoing challenge in molecular cancer studies. Here, we probe the GTP-bound K-Ras4B conformational dynamics using long-time ... ...

Abstract	Classifying reliably active and inactive molecular conformations of wildtype (WT) and mutated oncogenic proteins is a key, ongoing challenge in molecular cancer studies. Here, we probe the GTP-bound K-Ras4B conformational dynamics using long-time atomistic molecular dynamics (MD) simulations. We extract and analyze the detailed underlying free energy landscape of WT K-Ras4B. We use two key reaction coordinates, labeled d
MeSH term(s)	Molecular Dynamics Simulation ; Molecular Conformation ; Guanosine Triphosphate/chemistry ; Guanosine Triphosphate/metabolism
Chemical Substances	Guanosine Triphosphate (86-01-1)
Language	English
Publishing date	2023-02-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0139181
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Article ; Online: Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning.

Narayan, Brajesh / Buchete, Nicolae-Viorel / Elber, Ron

The journal of physical chemistry. B

2021 Volume 125, Issue 22, Page(s) 5706–5715

Abstract: Gleevec (a.k.a., imatinib) is an important anticancer (e.g., chronic myeloid leukemia) chemotherapeutic drug due to its inhibitory interaction with the Abl kinase. Here, we use atomically detailed simulations within the Milestoning framework to study the ...

Abstract	Gleevec (a.k.a., imatinib) is an important anticancer (e.g., chronic myeloid leukemia) chemotherapeutic drug due to its inhibitory interaction with the Abl kinase. Here, we use atomically detailed simulations within the Milestoning framework to study the molecular dissociation mechanism of Gleevec from Abl kinase. We compute the dissociation free energy profile, the mean first passage time for unbinding, and explore the transition state ensemble of conformations. The milestones form a multidimensional network with average connectivity of about 2.93, which is significantly higher than the connectivity for a one-dimensional reaction coordinate. The free energy barrier for Gleevec dissociation is estimated to be ∼10 kcal/mol, and the exit time is ∼55 ms. We examined the transition state conformations using both, the committor and transition function. We show that near the transition state the highly conserved salt bridge K217 and E286 is transiently broken. Together with the calculated free energy profile, these calculations can advance the understanding of the molecular interaction mechanisms between Gleevec and Abl kinase and play a role in future drug design and optimization studies.
MeSH term(s)	Computer Simulation ; Humans ; Imatinib Mesylate ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy ; Molecular Conformation
Chemical Substances	Imatinib Mesylate (8A1O1M485B)
Language	English
Publishing date	2021-04-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c00264
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Article: Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning

Narayan, Brajesh / Buchete, Nicolae-Viorel / Elber, Ron

Journal of physical chemistry. 2021 Apr. 30, v. 125, no. 22

2021

Abstract	Gleevec (a.k.a., imatinib) is an important anticancer (e.g., chronic myeloid leukemia) chemotherapeutic drug due to its inhibitory interaction with the Abl kinase. Here, we use atomically detailed simulations within the Milestoning framework to study the molecular dissociation mechanism of Gleevec from Abl kinase. We compute the dissociation free energy profile, the mean first passage time for unbinding, and explore the transition state ensemble of conformations. The milestones form a multidimensional network with average connectivity of about 2.93, which is significantly higher than the connectivity for a one-dimensional reaction coordinate. The free energy barrier for Gleevec dissociation is estimated to be ∼10 kcal/mol, and the exit time is ∼55 ms. We examined the transition state conformations using both, the committor and transition function. We show that near the transition state the highly conserved salt bridge K217 and E286 is transiently broken. Together with the calculated free energy profile, these calculations can advance the understanding of the molecular interaction mechanisms between Gleevec and Abl kinase and play a role in future drug design and optimization studies.
Keywords	Gibbs free energy ; computers ; dissociation ; drug design ; drug therapy ; drugs ; myeloid leukemia ; physical chemistry
Language	English
Dates of publication	2021-0430
Size	p. 5706-5715.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c00264
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Article ; Online: Unlocking the atomic-level details of amyloid fibril growth through advanced biomolecular simulations.

Buchete, Nicolae-Viorel

Biophysical journal

2012 Volume 103, Issue 7, Page(s) 1411–1413

MeSH term(s)	Amyloid/chemistry ; Kinetics ; Models, Molecular ; Protein Multimerization ; Protein Structure, Secondary ; Thermodynamics
Chemical Substances	Amyloid
Language	English
Publishing date	2012-10-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2012.08.052
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Article ; Online: Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields.

Narayan, Brajesh / Herbert, Colm / Rodriguez, Brian J / Brooks, Bernard R / Buchete, Nicolae-Viorel

The journal of physical chemistry. B

2021 Volume 125, Issue 20, Page(s) 5233–5242

Abstract: The self-assembling propensity of amyloid peptides such as diphenylalanine (FF) allows them to form ordered, nanoscale structures, with biocompatible properties important for biomedical applications. Moreover, piezoelectric properties allow FF molecules ... ...

Abstract	The self-assembling propensity of amyloid peptides such as diphenylalanine (FF) allows them to form ordered, nanoscale structures, with biocompatible properties important for biomedical applications. Moreover, piezoelectric properties allow FF molecules and their aggregates (e.g., FF nanotubes) to be aligned in a controlled way by the application of external electric fields. However, while the behavior of FF nanostructures emerges from the biophysical properties of the monomers, the detailed responses of individual peptides to both temperature and electric fields are not fully understood. Here, we study the temperature-dependent conformational dynamics of FF peptides solvated in explicit water molecules, an environment relevant to biomedical applications, by using an enhanced sampling method, replica exchange molecular dynamics (REMD), in conjunction with applied electric fields. Our simulations highlight and overcome possible artifacts that may occur during the setup of REMD simulations of explicitly solvated peptides in the presence of external electric fields, a problem particularly important in the case of short peptides such as FF. The presence of the external fields could overstabilize certain conformational states in one or more REMD replicas, leading to distortions of the underlying potential energy distributions observed at each temperature. This can be overcome by correcting the REMD initial conditions to include the lower-energy conformations induced by the external field. We show that the converged REMD data can be analyzed using a Markovian description of conformational states and show that a rather complex, 3-state, temperature-dependent conformational dynamics in the absence of electric fields collapses to only one of these states in the presence of the electric fields. These details on the temperature- and electric-field-dependent thermodynamic and kinetic properties of small FF amyloid peptides can be useful in understanding and devising new methods to control their aggregation-prone biophysical properties and, possibly, the structural and biophysical properties of FF molecular nanostructures.
MeSH term(s)	Amyloidogenic Proteins ; Molecular Dynamics Simulation ; Peptides ; Phenylalanine
Chemical Substances	Amyloidogenic Proteins ; Peptides ; diphenylalanine ; Phenylalanine (47E5O17Y3R)
Language	English
Publishing date	2021-05-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c01939
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Article ; Online: Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions.

Duffy, Fergal / Maheshwari, Nikunj / Buchete, Nicolae-Viorel / Shields, Denis

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2001, Page(s) 73–95

Abstract: Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by ...

Abstract	Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.
MeSH term(s)	Biophysical Phenomena ; Computational Biology ; Computational Chemistry ; Cyclization ; Drug Discovery ; Molecular Dynamics Simulation ; Peptide Library ; Peptides, Cyclic/chemistry ; Peptides, Cyclic/metabolism ; Protein Conformation ; Protein Interaction Mapping
Chemical Substances	Peptide Library ; Peptides, Cyclic
Language	English
Publishing date	2019-05-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9504-2_5
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Article ; Online: Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning.

Narayan, Brajesh / Yuan, Ye / Fathizadeh, Arman / Elber, Ron / Buchete, Nicolae-Viorel

Progress in molecular biology and translational science

2020 Volume 170, Page(s) 215–237

Abstract: Molecular dynamics (MD) studies of biomolecules require the ability to simulate complex biochemical systems with an increasingly larger number of particles and for longer time scales, a problem that cannot be overcome by computational hardware advances ... ...

Abstract	Molecular dynamics (MD) studies of biomolecules require the ability to simulate complex biochemical systems with an increasingly larger number of particles and for longer time scales, a problem that cannot be overcome by computational hardware advances alone. A main problem springs from the intrinsically high-dimensional and complex nature of the underlying free energy landscape of most systems, and from the necessity to sample accurately such landscapes for identifying kinetic and thermodynamic states in the configurations space, and for accurate calculations of both free energy differences and of the corresponding transition rates between states. Here, we review and present applications of two increasingly popular methods that allow long-time MD simulations of biomolecular systems that can open a broad spectrum of new studies. A first approach, Markov State Models (MSMs), relies on identifying a set of configuration states in which the system resides sufficiently long to relax and loose the memory of previous transitions, and on using simulations for mapping the underlying complex energy landscape and for extracting accurate thermodynamic and kinetic information. The Markovian independence of the underlying transition probabilities creates the opportunity to increase the sampling efficiency by using sets of appropriately initialized short simulations rather than typically long MD trajectories, which also enhances sampling. This allows MSM-based studies to unveil bio-molecular mechanisms and to estimate free energy barriers with high accuracy, in a manner that is both systematic and relatively automatic, which accounts for their increasing popularity. The second approach presented, Milestoning, targets accurate studies of the ensemble of pathways connecting specific end-states (e.g., reactants and products) in a similarly systematic, accurate and highly automatic manner. Applications presented range from studies of conformational dynamics and binding of amyloid-forming peptides, cell-penetrating peptides and the DFG-flip dynamics in Abl kinase. As highlighted by the increasing number of studies using both methods, we anticipate that they will open new avenues for the investigation of systematic sampling of reactions pathways and mechanisms occurring on longer time scales than currently accessible by purely computational hardware developments.
MeSH term(s)	Markov Chains ; Molecular Dynamics Simulation ; Phosphatidylcholines/chemistry
Chemical Substances	Phosphatidylcholines ; 1,2-oleoylphosphatidylcholine (EDS2L3ODLV)
Language	English
Publishing date	2020-02-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2471995-X
ISSN	1878-0814 ; 0079-6603 ; 1877-1173
ISSN (online)	1878-0814
ISSN	0079-6603 ; 1877-1173
DOI	10.1016/bs.pmbts.2020.01.002
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Article: The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning

Narayan, Brajesh / Fathizadeh, Arman / Templeton, Clark / He, Peng / Arasteh, Shima / Elber, Ron / Buchete, Nicolae-Viorel / Levy, Ron M

Elsevier B.V. Biochimica et biophysica acta. 2020 Apr., v. 1864, no. 4

2020

Abstract: Kinases are a family of enzymes that catalyze the transfer of the ɤ-phosphate group from ATP to a protein's residue. Malfunctioning kinases are involved in many health problems such as cardiovascular diseases, diabetes, and cancer. Kinases transitions ... ...

Abstract	Kinases are a family of enzymes that catalyze the transfer of the ɤ-phosphate group from ATP to a protein's residue. Malfunctioning kinases are involved in many health problems such as cardiovascular diseases, diabetes, and cancer. Kinases transitions between multiple conformations of inactive to active forms attracted considerable interest.A reaction coordinate is computed for the transition between the active to inactive conformation in Abl kinase with a focus on the DFG-in to DFG-out flip. The method of Rock Climbing is used to construct a path locally, which is subsequently optimized using a functional of the entire path. The discrete coordinate sets along the reaction path are used in a Milestoning calculation of the free energy landscape and the rate of the transition.The estimated transition times are between a few milliseconds and seconds, consistent with simulations of the kinetics and with indirect experimental data. The activation requires the transient dissociation of the salt bridge between Lys271 and Glu286. The salt bridge reforms once the DFG motif is stabilized by a locked conformation of Phe382. About ten residues are identified that contribute significantly to the process and are included as part of the reaction space.The transition from DFG-in to DFG-out in Abl kinase was simulated using atomic resolution of a fully solvated protein yielding detailed description of the kinetics and the mechanism of the DFG flip. The results are consistent with other computational methods that simulate the kinetics and with some indirect experimental measurements.The activation of kinases includes a conformational transition of the DFG motif that is important for enzyme activity but is not accessible to conventional Molecular Dynamics. We propose a detailed mechanism for the transition, at a timescale longer than conventional MD, using a combination of reaction path and Milestoning algorithms. The mechanism includes local structural adjustments near the binding site as well as collective interactions with more remote residues.
Keywords	Gibbs free energy ; adenosine triphosphate ; algorithms ; binding sites ; cardiovascular diseases ; computational methodology ; diabetes ; dissociation ; enzyme activity ; molecular dynamics ; neoplasms ; phosphotransferases (kinases)
Language	English
Dates of publication	2020-04
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	840755-1
ISSN	0304-4165
ISSN	0304-4165
DOI	10.1016/j.bbagen.2019.129508
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Article ; Online: Alzheimer Aβ peptide interactions with lipid membranes: fibrils, oligomers and polymorphic amyloid channels.

Tofoleanu, Florentina / Buchete, Nicolae-Viorel

Prion

2012 Volume 6, Issue 4, Page(s) 339–345

Abstract: Fibrillar aggregates of misfolded amyloid proteins are involved in a variety of diseases such as Alzheimer disease (AD), type 2 diabetes, Parkinson, Huntington and prion-related diseases. In the case of AD amyloid β (Aβ) peptides, the toxicity of amyloid ...

Abstract	Fibrillar aggregates of misfolded amyloid proteins are involved in a variety of diseases such as Alzheimer disease (AD), type 2 diabetes, Parkinson, Huntington and prion-related diseases. In the case of AD amyloid β (Aβ) peptides, the toxicity of amyloid oligomers and larger fibrillar aggregates is related to perturbing the biological function of the adjacent cellular membrane. We used atomistic molecular dynamics (MD) simulations of Aβ 9-40 fibrillar oligomers modeled as protofilament segments, including lipid bilayers and explicit water molecules, to probe the first steps in the mechanism of Aβ-membrane interactions. Our study identified the electrostatic interaction between charged peptide residues and the lipid headgroups as the principal driving force that can modulate the further penetration of the C-termini of amyloid fibrils or fibrillar oligomers into the hydrophobic region of lipid membranes. These findings advance our understanding of the detailed molecular mechanisms and the effects related to Aβ-membrane interactions, and suggest a polymorphic structural character of amyloid ion channels embedded in lipid bilayers. While inter-peptide hydrogen bonds leading to the formation of β-strands may still play a stabilizing role in amyloid channel structures, these may also present a significant helical content in peptide regions (e.g., termini) that are subject to direct interactions with lipids rather than with neighboring Aβ peptides.
MeSH term(s)	Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/metabolism ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Cell Membrane/pathology ; Humans ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; Molecular Dynamics Simulation
Chemical Substances	Amyloid beta-Peptides ; Lipid Bilayers
Language	English
Publishing date	2012-08-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267671-5
ISSN	1933-690X ; 1933-690X
ISSN (online)	1933-690X
ISSN	1933-690X
DOI	10.4161/pri.21022
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Article ; Online: Molecular interactions of Alzheimer's Aβ protofilaments with lipid membranes.

Tofoleanu, Florentina / Buchete, Nicolae-Viorel

Journal of molecular biology

2012 Volume 421, Issue 4-5, Page(s) 572–586

Abstract: Amyloid fibrils and peptide oligomers play central roles in the pathology of Alzheimer's disease, type 2 diabetes, Parkinson's disease, Huntington's disease, and prion-related disease. Here, we investigate the molecular interactions between preformed ... ...

Abstract	Amyloid fibrils and peptide oligomers play central roles in the pathology of Alzheimer's disease, type 2 diabetes, Parkinson's disease, Huntington's disease, and prion-related disease. Here, we investigate the molecular interactions between preformed amyloid β (Aβ) molecular protofilaments and lipid bilayer membranes, in the presence of explicit water molecules, using computational models and all-atom molecular dynamics. These interactions play an important role in the stability and function of both Aβ fibrils and the adjacent cellular membrane. Taking advantage of the symmetry-related and directional properties of the protofilaments, we build models that cover several relative protofilament-membrane orientations. Our molecular dynamics simulations reveal the relative contributions of different structural elements to the dynamics and stability of Aβ protofilament segments near membranes, and the first steps in the mechanism of fibril-membrane interactions. During this process, we observe a significant alteration of the side-chain contact pattern in protofilaments, although a fraction of the characteristic β-sheet content is preserved. As a major driving force, we identify the electrostatic interactions between Aβ charged side chains, including E22, D23, and K28, and lipid headgroups. Together with hydrogen bonding with atoms from lipid headgroups, these interactions can facilitate the penetration of hydrophobic C-terminal amino acids through the lipid headgroup region, which can finally lead both to further loss of the initial fibril structure and to local membrane-thinning effects. Our results may guide new experiments that could test the extent to which the structural features of water-formed amyloid fibrils are preserved, lost, or reshaped by membrane-mediated interactions.
MeSH term(s)	Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/metabolism ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; Membranes/chemistry ; Membranes/metabolism ; Models, Chemical ; Models, Molecular ; Molecular Conformation ; Molecular Dynamics Simulation ; Multiprotein Complexes/metabolism ; Protein Binding ; Static Electricity ; Water/metabolism
Chemical Substances	Amyloid beta-Peptides ; Lipid Bilayers ; Multiprotein Complexes ; Water (059QF0KO0R)
Language	English
Publishing date	2012-08-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2011.12.063
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