Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

Xu, Dong; Zhang, Yang

doi:10.1016/j.bpj.2011.10.024

Cited by 937 publications

(650 citation statements)

References 28 publications

Supporting

Mentioning

640

Contrasting

Unclassified

Order By: Relevance

“…The lowest free energy conformations were determined by SPICKER (a clustering approach to identify near-native protein folds; Zhang and Skolnick, 2004). Refinement of the low free energy conformations was done by using FG-MD (Fragment Guided Molecular Dynamics simulations; Zhang et al, 2011) and ModRefiner (Xu and Zhang, 2011). Prediction of the ligand-binding site of the target protein was made by COACH algorithm (Yang et al, 2013).…”

Section: Myoglobin Modelingmentioning

confidence: 99%

Species-Specificity in Myoglobin Oxygenation and Reduction Potential Properties

Nerimetla

Krishnan

Mazumder

et al. 2017

Meat and Muscle Biology

View full text Add to dashboard Cite

Abstract:The objective was to compare oxygenation and reduction potential properties of bovine and porcine myoglobins in-vitro. Cyclic voltammetry and homology-based myoglobin modeling were used to determine the species-specific effects on myoglobin reduction potential and oxygenation properties at pH 5.6, 6.4, and 7.4. At all pHs, porcine myoglobin had greater (P = 0.04) oxygen affinity than bovine myoglobin. For both species, oxygen affinity was higher at pH 6.4 > pH 7.4 > 5.6 (P = 0.0002). Myoglobin reduction potential for both species was affected by pH (P < 0.0001). The redox potentials became more negative as pH increased, indicating a proton-coupled electron transfer. There were no differences (P = 0.51) between species in reduction potential properties of heme. Homology-based myoglobin modeling indicated that the porcine myoglobin has a shorter distance between the distal histidine and heme than does bovine myoglobin. The variation in amino acid composition between bovine and porcine myoglobin could be partially responsible for differences in oxygen affinity.

show abstract

Section: Myoglobin Modelingmentioning

confidence: 99%

Species-Specificity in Myoglobin Oxygenation and Reduction Potential Properties

Nerimetla

Krishnan

Mazumder

et al. 2017

Meat and Muscle Biology

View full text Add to dashboard Cite

show abstract

“…The Ramachandran plot displays the main chain conformation angles (Phi and Psi) of the polypeptide chain of a protein molecule. One predicted model with the highest score was selected as the structural model of beta-barrel domain of AbOmpA and then energy minimization refinements were performed at Modrefiner online tool (a high-resolution protein structure refinement web server [19]). The refined model was validated by PorSA web server (an interactive web service for the recognition of errors in three-dimensional structures of proteins [20]).…”

Section: Methodsmentioning

confidence: 99%

Molecular analysis of AbOmpA type-1 as immunogenic target for therapeutic interventions against MDR Acinetobacter baumannii infection

Badmasti

Siadat

Bouzari

et al. 2015

vacres

View full text Add to dashboard Cite

Introduction: Acinetobacter baumannii is associated with hospital-acquired infections. Outer membrane protein A of A.baumannii (AbOmpA) is a well-characterized virulence factor which has important roles in pathogenesis of this bacterium. Methods: Based on our PCR-sequencing of ompA gene in the clinical isolates, AbOmpA protein can be categorized into two types, named here type-1 and type-2. We are performed in silico analyses on beta-barrel domain of AbOmpA such as sequence alignments, prediction of 3D modeling and immunoinformatics. Results: High prevalence of AbOmpA type-1 were detected both in 21 multidrug-resistant (MDR) A. baumannii isolates collected from clinical settings (64% of total sequences) and in silico sequences extracted from Uniprot database (49.7% of total sequences). Multiple sequence alignments and phylogenic tree revealed AbOmpA sequences in comparison with OmpA of Enterobacteriaceae family were more heterogenic, especially at extracellular loops amino acid positions and were evolutionary far from this family. Characterization of in silico 3D molecular model of beta-barrel domain of AbOmpA type-1 showed this domain had four large extracellular loops which resemble to beta-barrel domain of Klebsiella pneumonia OmpA (KpOmpA). Immunoinformatics analyses showed the four extracellular loops had high scores as B and T cell antigenic epitopes especially in loop-1 and 3. Geometry analyses revealed extracellular loops effectively protrude to outer space of the cell. Conclusion: Beta-barrel domain of AbOmpA type-1 has all the characteristics of a promising vaccine and could be considered as an excellent target for a vaccine against MDR A. baumannii infection.

show abstract

“…The three dimensional (3D) model for CCT5 protein ( Figure 3) was generated by Phyre2 server and the model refinement and energy minimization was done by ModRefiner program that utilizes an algorithm for atomic level to develop and refine protein structures, critically based on a two-step, atomic-level energy minimization [22]. Ramachandran plot of model as illustrated in Figure 4 was analyzed by RAMPAGE server and overall G factor from PROCHECK.…”

Section: Determination Of Cct5 Tertiary Structurementioning

confidence: 99%

Computational Analysis of HSP-60 Protein with Structural Insights into Chaperonin Containing TCP-1 Subunit 5 in Bos Taurus

Singh¹,

Kumar²,

Rajesh³

et al. 2017

MOJPB

View full text Add to dashboard Cite

Heat shock protein 60 kDa (HSP60) is a crucial chaperone that guides appropriate folding of denatured proteins under heat stress conditions. HSP60 provides assistance in correct folding of a multitude of denatured proteins. The Group II eukaryotic chaperonin TCP-1 ring complex is (TRiC or CCT) important cytosolic chaperonin which plays important role in folding of essential subset of cytosolic proteins and is believed to be highly conserved among different eukaryotic species. In this study, an extensive in silico analysis has been performed ranging from sequence comparison among species to homology modeling of Bos taurus Cct5 protein and determination of Hsp60 interacting partners. The comparative analysis of the protein revealed certain significant variations in Bos taurus. The experimental protein structure for Cct5 in Bos taurus is unknown till date, therefore the putative protein structure was determined using homology modeling. The stereo chemical properties of protein were assessed by utilizing several scrutiny tools such as PROCHECK, VERIFY3D and RAMPAGE to ensure model accuracy. The mode of interaction between HSF1 and Cct5 protein was evaluated by molecular docking studies.

show abstract

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

Cited by 937 publications

References 28 publications

Species-Specificity in Myoglobin Oxygenation and Reduction Potential Properties

Species-Specificity in Myoglobin Oxygenation and Reduction Potential Properties

Molecular analysis of AbOmpA type-1 as immunogenic target for therapeutic interventions against MDR Acinetobacter baumannii infection

Computational Analysis of HSP-60 Protein with Structural Insights into Chaperonin Containing TCP-1 Subunit 5 in Bos Taurus

Contact Info

Product

Resources

About