scholarly journals Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

2018 ◽  
Author(s):  
Elena Papaleo ◽  
Carlo Camilloni ◽  
Kaare Teilum ◽  
Michele Vendruscolo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Force Field ◽  
Chemical Shifts ◽  
Molten Globule ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Structural Heterogeneity ◽  
Order Parameters ◽  
Protein Domain ◽  
Conformational Ensemble ◽  
Native State

ABSTRACTMany proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of confor-mations, it is important to be able to generate models of native state ensembles with high accuracy. Due to limitations in sampling efficiency and force field accuracy it is, however, challenging to obtain accurate ensembles of protein conformations by the use of molecular simulations alone. Here we show that dynamic ensemble refinement, which combines an accurate atomistic force field with commonly available nuclear magnetic resonance (NMR) chemical shifts and NOEs, can provide a detailed and accurate description of the conformational ensemble of the native state of a highly dynamic protein. As both NOEs and chemical shifts are averaged on timescales up to milliseconds, the resulting ensembles reflect the structural heterogeneity that goes beyond that probed e.g. by NMR relaxation order parameters. We selected the small protein domain NCBD as object of our study since this protein, which has been characterized experimentally in substantial detail, displays a rich and complex dynamical behaviour. In particular, the protein has been described as having a molten-globule like structure, but with a relatively rigid core. Our approach allowed us to describe the conformational dynamics of NCBD in solution, and to probe the structural heterogeneity resulting from both short- and long-time-scale dynamics by the calculation of order parameters on different time scales. These results illustrate the usefulness of our approach since they show that NCBD is rather rigid on the nanosecond timescale, but interconverts within a broader ensemble on longer timescales, thus enabling the derivation of a coherent set of conclusions from various NMR experiments on this protein, which could otherwise appear in contradiction with each other.

scholarly journals Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5125 ◽  
Author(s):  
Elena Papaleo ◽  
Carlo Camilloni ◽  
Kaare Teilum ◽  
Michele Vendruscolo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Force Field ◽  
Chemical Shifts ◽  
Molten Globule ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Structural Heterogeneity ◽  
Order Parameters ◽  
Protein Domain ◽  
Conformational Ensemble ◽  
Native State

Many proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of conformations, it is important to be able to generate models of native state ensembles with high accuracy. Due to limitations in sampling efficiency and force field accuracy it is, however, challenging to obtain accurate ensembles of protein conformations by the use of molecular simulations alone. Here we show that dynamic ensemble refinement, which combines an accurate atomistic force field with commonly available nuclear magnetic resonance (NMR) chemical shifts and NOEs, can provide a detailed and accurate description of the conformational ensemble of the native state of a highly dynamic protein. As both NOEs and chemical shifts are averaged on timescales up to milliseconds, the resulting ensembles reflect the structural heterogeneity that goes beyond that probed, e.g., by NMR relaxation order parameters. We selected the small protein domain NCBD as object of our study since this protein, which has been characterized experimentally in substantial detail, displays a rich and complex dynamical behaviour. In particular, the protein has been described as having a molten-globule like structure, but with a relatively rigid core. Our approach allowed us to describe the conformational dynamics of NCBD in solution, and to probe the structural heterogeneity resulting from both short- and long-timescale dynamics by the calculation of order parameters on different time scales. These results illustrate the usefulness of our approach since they show that NCBD is rather rigid on the nanosecond timescale, but interconverts within a broader ensemble on longer timescales, thus enabling the derivation of a coherent set of conclusions from various NMR experiments on this protein, which could otherwise appear in contradiction with each other.

Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

2021 ◽  
Author(s):  
Yulian Gavrilov ◽  
Felix Kümmerer ◽  
Simone Orioli ◽  
Andreas Prestel ◽  
Kresten Lindorff-Larsen ◽  
...  
Keyword(s):  
Double Mutant ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Conformational Heterogeneity ◽  
Native State ◽  
Chymotrypsin Inhibitor 2 ◽  
Relaxation Measurements ◽  
The Stability ◽  
Dynamics Simulations ◽  
Mutant Forms

The conformational heterogeneity of a folded protein can affect both its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here we have examined whether changed native state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side-chains with molecular dynamics simulations to quantify the native state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: A reduction in conformational dynamics (and entropy) of the native state of L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native state entropy might be needed to improve the predictions of the effect of mutations on protein stability.

CONFORMATIONAL DYNAMICS OF HIV-1 PROTEASE: A COMPARATIVE MOLECULAR DYNAMICS SIMULATION STUDY WITH MULTIPLE AMBER FORCE FIELDS

2012 ◽  
Vol 10 (06) ◽  
pp. 1250018 ◽  
Author(s):  
BISWA RANJAN MEHER ◽  
MATTAPARTHI VENKATA SATISH KUMAR ◽  
SMRITI SHARMA ◽  
PRADIPTA BANDYOPADHYAY
Keyword(s):  
Force Field ◽  
Active Site ◽  
Force Fields ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Order Parameters ◽  
Dynamics Simulation ◽  
Active Site Cavity ◽  
Amber Force Fields ◽  
Hiv 1

Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.

Conformational dynamics and thermodynamics of protein–ligand binding studied by NMR relaxation

2012 ◽  
Vol 40 (2) ◽  
pp. 419-423 ◽  
Author(s):  
Mikael Akke
Keyword(s):  
Ligand Binding ◽  
Bound States ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Titration Calorimetry ◽  
Conformational Entropy ◽  
Chain Order ◽  
Ligand Interactions ◽  
Galectin 3 ◽  
Relaxation Experiments

Protein conformational dynamics can be critical for ligand binding in two ways that relate to kinetics and thermodynamics respectively. First, conformational transitions between different substates can control access to the binding site (kinetics). Secondly, differences between free and ligand-bound states in their conformational fluctuations contribute to the entropy of ligand binding (thermodynamics). In the present paper, I focus on the second topic, summarizing our recent results on the role of conformational entropy in ligand binding to Gal3C (the carbohydrate-recognition domain of galectin-3). NMR relaxation experiments provide a unique probe of conformational entropy by characterizing bond-vector fluctuations at atomic resolution. By monitoring differences between the free and ligand-bound states in their backbone and side chain order parameters, we have estimated the contributions from conformational entropy to the free energy of binding. Overall, the conformational entropy of Gal3C increases upon ligand binding, thereby contributing favourably to the binding affinity. Comparisons with the results from isothermal titration calorimetry indicate that the conformational entropy is comparable in magnitude to the enthalpy of binding. Furthermore, there are significant differences in the dynamic response to binding of different ligands, despite the fact that the protein structure is virtually identical in the different protein–ligand complexes. Thus both affinity and specificity of ligand binding to Gal3C appear to depend in part on subtle differences in the conformational fluctuations that reflect the complex interplay between structure, dynamics and ligand interactions.

The Native State Conformational Ensemble of the SH3 Domain from α-Spectrin†

Biochemistry ◽  
1999 ◽  
Vol 38 (28) ◽  
pp. 8899-8906 ◽  
Author(s):  
Mourad Sadqi ◽  
Salvador Casares ◽  
María A. Abril ◽  
Obdulio López-Mayorga ◽  
Francisco Conejero-Lara ◽  
...  
Keyword(s):  
Sh3 Domain ◽  
Conformational Ensemble ◽  
Native State

scholarly journals Starting Structure Dependence of NMR Order Parameters Derived from MD Simulations: Implications for Judging Force-Field Quality

2008 ◽  
Vol 95 (1) ◽  
pp. L04-L06 ◽  
Author(s):  
Alrun N. Koller ◽  
Harald Schwalbe ◽  
Holger Gohlke
Keyword(s):  
Force Field ◽  
Md Simulations ◽  
Order Parameters ◽  
Structure Dependence ◽  
Field Quality

scholarly journals Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?

2017 ◽  
Vol 13 (1) ◽  
pp. e1005314 ◽  
Author(s):  
Christopher M. Siwy ◽  
Christopher Lockhart ◽  
Dmitri K. Klimov
Keyword(s):  
Force Field ◽  
Conformational Ensemble ◽  
Field Dependent

scholarly journals Synthesis runs counter to directional folding of a nascent protein domain

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiuqi Chen ◽  
Nandakumar Rajasekaran ◽  
Kaixian Liu ◽  
Christian M. Kaiser
Keyword(s):  
Single Molecule ◽  
Molten Globule ◽  
Elongation Factor ◽  
Protein Domain ◽  
Folding Pathway ◽  
Native Structure ◽  
Folding Intermediates ◽  
C Terminus

Abstract Folding of individual domains in large proteins during translation helps to avoid otherwise prevalent inter-domain misfolding. How folding intermediates observed in vitro for the majority of proteins relate to co-translational folding remains unclear. Combining in vivo and single-molecule experiments, we followed the co-translational folding of the G-domain, encompassing the first 293 amino acids of elongation factor G. Surprisingly, the domain remains unfolded until it is fully synthesized, without collapsing into molten globule-like states or forming stable intermediates. Upon fully emerging from the ribosome, the G-domain transitions to its stable native structure via folding intermediates. Our results suggest a strictly sequential folding pathway initiating from the C-terminus. Folding and synthesis thus proceed in opposite directions. The folding mechanism is likely imposed by the final structure and might have evolved to ensure efficient, timely folding of a highly abundant and essential protein.

scholarly journals Synthesis runs counter to directional folding of a nascent protein domain

2020 ◽  
Author(s):  
Xiuqi Chen ◽  
Nandakumar Rajasekaran ◽  
Kaixian Liu ◽  
Christian M. Kaiser
Keyword(s):  
Single Molecule ◽  
Molten Globule ◽  
Elongation Factor ◽  
Protein Domain ◽  
Folding Pathway ◽  
Native Structure ◽  
Folding Intermediates ◽  
C Terminus

AbstractFolding of individual domains in large proteins during translation helps to avoid otherwise prevalent inter-domain misfolding. How folding intermediates observed in vitro for the majority of proteins relate to co-translational folding remains unclear. Combining in vivo and single-molecule experiments, we followed the co-translational folding of the G-domain, encompassing the first 293 amino acids of elongation factor G. Surprisingly, the domain remains unfolded until it is fully synthesized, without collapsing into molten globule-like states or forming stable intermediates. Upon fully emerging from the ribosome, the G-domain transitions to its stable native structure via folding intermediates. Our results suggest a strictly sequential folding pathway initiating from the C-terminus. Folding and synthesis thus proceed in opposite directions. The folding mechanism is likely imposed by the final structure and might have evolved to ensure efficient, timely folding of a highly abundant and essential protein.

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