Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

Srivastava, Ashutosh; Nagai, Tetsuro; Srivastava, Arpita; Miyashita, Osamu; Tama, Florence

doi:10.3390/ijms19113401

Cited by 69 publications

(55 citation statements)

References 198 publications

(217 reference statements)

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“…Modelling the full-length KIT cytoplasmic domain. Progress in computational algorithms and technique has enabled in depth study of protein molecular structure and dynamics using limited experimental data [14][15][16][17] . The model is built based on a known 3D homologous protein structure is at present the widely used approach.…”

Section: Resultsmentioning

confidence: 99%

“…Four candidate models (M1, M2, M3 and M4) of the full-length KIT cytoplasmic domain were explored by all-atoms MD simulations. Since the success of MD simulations over a ten to hundreds of nanoseconds time scale for the refinement of homology or ab initio models of small to medium-size proteins was demonstrated 14,15,17,19 , we expected that the 500-ns MD simulations may be pertinent when scanning a conformational stability of the alternative KIT models. We suggest that such simulation time would allow the equilibrated state of the protein to be reached for a biologically relevant model.…”

Section: Resultsmentioning

confidence: 99%

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The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor

Inizan

Hanna

Stolyarchuk

et al. 2020

Sci Rep

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Receptor tyrosine kinases (RTKs) are key regulators of normal cellular processes and have a critical role in the development and progression of many diseases. RTK ligand-induced stimulation leads to activation of the cytoplasmic kinase domain that controls the intracellular signalling. Although the kinase domain of RTKs has been extensively studied using X-ray analysis, the kinase insert domain (KID) and the C-terminal are partially or fully missing in all reported structures. We communicate the first structural model of the full-length RTK KIT cytoplasmic domain, a crucial target for cancer therapy. This model was achieved by integration of ab initio KID and C-terminal probe models into an X-ray structure, and by their further exploration through molecular dynamics (MD) simulation. An extended (2-µs) MD simulation of the proper model provided insight into the structure and conformational dynamics of the full-length cytoplasmic domain of KIT, which can be exploited in the description of the KIT transduction processes. Receptor Tyrosine Kinases (RTKs) are cell-surface transmembrane proteins that control cell-signalling pathways 1 .

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor

Inizan

Hanna

Stolyarchuk

et al. 2020

Sci Rep

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“…This is perhaps not surprising as crystal structures tend to capture averaged enzyme conformations which may be catalytically deficient. 45,46 Additionally, in the OXA-48-ceftazadime complex structure, triethylene glycol is co-crystallized in the space occupied by the Ω-loop in the apoenzyme, which interactions with an oxyanion hole, 47 in OXA-48 formed by the backbone amides of Ser70 and Tyr211, 12 stabilize TI formation in β-lactamases (similar to many other co-factor independent hydrolases). Thus, hydrogen bond distances between these residues and the ceftazidime AE were measured in both the extended MM MD and QM/MM MD simulations and are shown in the ESI (S8-S11).…”

Section: Oxa-181 R214smentioning

confidence: 99%

Small Changes in Hydration Determine Cephalosporinase Activity of OXA-48 β-Lactamases

Hirvonen¹,

Mulholland²,

Spencer³

et al. 2020

Preprint

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<p>β-lactamase mediated antibiotic resistance threatens treatment of bacterial infections. OXA-48 enzymes are clinically important class D serine β-lactamases (SBLs) that confer resistance to most β-lactam antibiotics, including carbapenems. However, OXA-48 and related enzymes vary widely in their activity towards different substrates: OXA-48 primarily hydrolyzes carbapenems, whereas the OXA-163 variant is a cephalosporinase with minimal carbapenemase activity. The basis of cephalosporinase activity in OXA-163 remains elusive. Here we use QM/MM reaction simulations (umbrella sampling molecular dynamics) to study breakdown of the cephalosporin antibiotic ceftazidime, a key antibiotic for healthcare-associated infections, by selected OXA-48 variants. Calculated free energy barriers for ceftazidime deacylation correctly capture the differing catalytic efficiencies of the studied enzymes and identify the catalytically competent orientation for bound ceftazidime. Additionally, we show that high flexibility of the Ω-loop bordering the active site, a determinant of specificity in many SBLs, is not required for efficient deacylation. Based on our simulations, cephalosporin breakdown in OXA-163 is efficient due to subtle control of active site solvation, which requires a particular orientation of Leu158 in the Ω-loop. Our simulations further predict that a single mutation in the OXA-48 β5 - β6 loop (Arg214Ser) will increase the efficiency of ceftazidime deacylation to that of OXA-163. The finding that the hydration of the general base in the active site determines deacylation efficiency is possibly important in other class D β-lactamases.<br></p>

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“…Macromolecules of the epigenome, especially linear peptide tails of histones and RNAs [113] often adopt various binding conformations imposing further challenges on structure determination methods. Histone tails are linear structures, which are seldom compatible with X-ray crystallographic approaches [114] since these experimental methods are better at handling globular structures that can be crystallized [114,115]. Such linear peptides are better accessed by X-ray crystallography, when they are a part of a globular structure, like a nucleosome.…”

Section: Conformational Diversity and Water-mediated Weak Interactionsmentioning

confidence: 99%

Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome

Zsidó

Hetényi

2020

IJMS

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Development of valid structure–activity relationships (SARs) is a key to the elucidation of pathomechanisms of epigenetic diseases and the development of efficient, new drugs. The present review is based on selected methodologies and applications supplying molecular structure, binding affinity and biological activity data for the development of new SARs. An emphasis is placed on emerging trends and permanent challenges of new discoveries of SARs in the context of proteins as epigenetic drug targets. The review gives a brief overview and classification of the molecular background of epigenetic changes, and surveys both experimental and theoretical approaches in the field. Besides the results of sophisticated, cutting edge techniques such as cryo-electron microscopy, protein crystallography, and isothermal titration calorimetry, examples of frequently used assays and fast screening techniques are also selected. The review features how different experimental methods and theoretical approaches complement each other and result in valid SARs of the epigenome.

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Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

Cited by 69 publications

References 198 publications

The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor

The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor

Small Changes in Hydration Determine Cephalosporinase Activity of OXA-48 β-Lactamases

Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome

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