Folding Intermediates, Heterogeneous Native Ensembles and Protein Function

Naganathan, Athi N.; Dani, R. El; Gopi, Soundhararajan; Aranganathan, Akashnathan; Narayan, Abhishek

doi:10.1016/j.jmb.2021.167325

Cited by 10 publications

(18 citation statements)

References 99 publications

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“…The block version of the Wako–Saitô–Muñoz–Eaton model (bWSME) was employed by fixing the parameters to those from a recent analysis of NQO1 folding thermodynamics [ 23 ]. A detailed description of the model and model parameterization has been provided in a recent work [ 24 ].…”

Section: Methodsmentioning

confidence: 99%

Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations

et al. 2022

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Allosterism is a common phenomenon in protein biochemistry that allows rapid regulation of protein stability; dynamics and function. However, the mechanisms by which allosterism occurs (by mutations or post-translational modifications (PTMs)) may be complex, particularly due to long-range propagation of the perturbation across protein structures. In this work, we have investigated allosteric communication in the multifunctional, cancer-related and antioxidant protein NQO1 by mutating several fully buried leucine residues (L7, L10 and L30) to smaller residues (V, A and G) at sites in the N-terminal domain. In almost all cases, mutated residues were not close to the FAD or the active site. Mutations L→G strongly compromised conformational stability and solubility, and L30A and L30V also notably decreased solubility. The mutation L10A, closer to the FAD binding site, severely decreased FAD binding affinity (≈20 fold vs. WT) through long-range and context-dependent effects. Using a combination of experimental and computational analyses, we show that most of the effects are found in the apo state of the protein, in contrast to other common polymorphisms and PTMs previously characterized in NQO1. The integrated study presented here is a first step towards a detailed structural–functional mapping of the mutational landscape of NQO1, a multifunctional and redox signaling protein of high biomedical relevance.

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Section: Methodsmentioning

confidence: 99%

Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations

et al. 2022

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“…The Wako-Saitô-Muñoz-Eaton (WSME) model based perturbation analysis of hPGK1 was performed as discussed before for mutants of the protein NQO1 58 . Briefly, an ensemble of 8,398,795 microstates is constructed employing the block-version of the WSME model-bWSME with a most probable block length of 5 consecutive residues-and the PDB structure 2XE7 59,60 . The microstate energetics include stabilizing contributions from van der Waals interactions (heavy-atom interactions identified with a 5 Å cut-off with a mean-field interaction energy of -78 J mol −1 per heavy atom contact), all-to-all electrostatics at pH 7 protonation state, and simplified solvation free energy (defined by the heat capacity change of − 0.36 J mol −1 K −1 per native contact).…”

Section: Proteolysis By Thermolysinmentioning

confidence: 99%

Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core

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Naganathan

et al. 2022

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Phosphoglycerate kinase has been a model for the stability, folding cooperativity and catalysis of a two-domain protein. The human isoform 1 (hPGK1) is associated with cancer development and rare genetic diseases that affect several of its features. To investigate how mutations affect hPGK1 folding landscape and interaction networks, we have introduced mutations at a buried site in the N-terminal domain (F25 mutants) that either created cavities (F25L, F25V, F25A), enhanced conformational entropy (F25G) or introduced structural strain (F25W) and evaluated their effects using biophysical experimental and theoretical methods. All F25 mutants folded well, but showed reduced unfolding cooperativity, kinetic stability and altered activation energetics according to the results from thermal and chemical denaturation analyses. These alterations correlated well with the structural perturbation caused by mutations in the N-terminal domain and the destabilization caused in the interdomain interface as revealed by H/D exchange under native conditions. Importantly, experimental and theoretical analyses showed that these effects are significant even when the perturbation is mild and local. Our approach will be useful to establish the molecular basis of hPGK1 genotype–phenotype correlations due to phosphorylation events and single amino acid substitutions associated with disease.

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“…Such multi-dimensional free-energy landscapes allow the visualization of detailed folding pathways. Moreover, the WSME model can predict the degree of structure formation of each residue along a folding pathway [ 26 , 79 , 80 , 81 ]. Using the WSME model with uniform contact energies, Sasai et al calculated the free-energy landscapes of the B domain of protein A (BdpA), consisting of three helices with a symmetric topology ( Figure 2 ) [ 26 ].…”

Section: Prediction Of Folding Mechanismsmentioning

confidence: 99%

“…In the previous sections, we showed that the folding mechanisms of small single-domain proteins are described well by the WSME model. By contrast, the folding mechanisms of multi-domain proteins have been less frequently studied because they have complex, multiple folding pathways and intermediates, making it difficult to theoretically predict the folding processes [ 53 , 75 , 78 , 81 , 91 , 106 , 108 , 112 , 113 , 114 , 115 , 116 ]. However, multi-domain proteins comprise the majority of the proteome, and more than 70% of eukaryotic proteins contain multiple domains [ 117 , 118 ].…”

Section: Folding Mechanisms Of Multi-domain Proteinsmentioning

confidence: 99%

The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics

2022

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Despite the recent advances in the prediction of protein structures by deep neutral networks, the elucidation of protein-folding mechanisms remains challenging. A promising theory for describing protein folding is a coarse-grained statistical mechanical model called the Wako–Saitô–Muñoz–Eaton (WSME) model. The model can calculate the free-energy landscapes of proteins based on a three-dimensional structure with low computational complexity, thereby providing a comprehensive understanding of the folding pathways and the structure and stability of the intermediates and transition states involved in the folding reaction. In this review, we summarize previous and recent studies on protein folding and dynamics performed using the WSME model and discuss future challenges and prospects. The WSME model successfully predicted the folding mechanisms of small single-domain proteins and the effects of amino-acid substitutions on protein stability and folding in a manner that was consistent with experimental results. Furthermore, extended versions of the WSME model were applied to predict the folding mechanisms of multi-domain proteins and the conformational changes associated with protein function. Thus, the WSME model may contribute significantly to solving the protein-folding problem and is expected to be useful for predicting protein folding, stability, and dynamics in basic research and in industrial and medical applications.

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Folding Intermediates, Heterogeneous Native Ensembles and Protein Function

Cited by 10 publications

References 99 publications

Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations

Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations

Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core

The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics

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