| scholarly article | Q13442814 |
| P356 | DOI | 10.1039/C7MT00216E |
| P698 | PubMed publication ID | 28967944 |
| P2093 | author name string | B Dedeoglu | |
| A R Atilgan | |||
| C Atilgan | |||
| H Abdizadeh | |||
| P2860 | cites work | Scalable rule-based modelling of allosteric proteins and biochemical networks | Q21145330 |
| Nonequilibrium Equality for Free Energy Differences | Q21698763 | ||
| A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis | Q22251297 | ||
| Unraveling of the E-helices and disruption of 4-fold pores are associated with iron mishandling in a mutant ferritin causing neurodegeneration | Q24318488 | ||
| Density-functional thermochemistry. III. The role of exact exchange | Q25938987 | ||
| Structure and dynamics of drug carriers and their interaction with cellular receptors: focus on serum transferrin | Q26853427 | ||
| Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation | Q27334938 | ||
| Mutation of the iron ligand His 249 to Glu in the N-lobe of human transferrin abolishes the dilysine "trigger" but does not significantly affect iron release | Q27621496 | ||
| Crystal structures of two mutants (K206Q, H207E) of the N-lobe of human transferrin with increased affinity for iron | Q27621931 | ||
| Atomically defined mechanism for proton transfer to a buried redox centre in a protein | Q27625054 | ||
| Crystal structures and iron release properties of mutants (K206A and K296A) that abolish the dilysine interaction in the N-lobe of human transferrin | Q27631474 | ||
| Crystallographic and biochemical analyses of the metal-free Haemophilus influenzae Fe3+-binding protein | Q27636905 | ||
| Structure of the human transferrin receptor-transferrin complex | Q27643181 | ||
| High-affinity binding by the periplasmic iron-binding protein from Haemophilus influenzae is required for acquiring iron from transferrin | Q27643871 | ||
| Structures of two mutants that probe the role in iron release of the dilysine pair in the N-lobe of human transferrin | Q27643931 | ||
| The role of vicinal tyrosine residues in the function of Haemophilus influenzae ferric-binding protein A | Q27664200 | ||
| Overdamped dynamics of folded protein domains within a locally harmonic basin using coarse graining based on a partition of compact flexible clusters | Q45789757 | ||
| Good practices in free-energy calculations | Q46484190 | ||
| Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions | Q46536865 | ||
| A mass spectrometric and molecular modelling study of cisplatin binding to transferrin | Q46729293 | ||
| The performance of semilocal and hybrid density functionals in 3d transition-metal chemistry | Q46929526 | ||
| Chelator-facilitated removal of iron from transferrin: relevance to combined chelation therapy | Q46964222 | ||
| Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential | Q47628195 | ||
| Binding of V(IV)O²⁺ to the Fe binding sites of human serum transferrin. A theoretical study | Q47744197 | ||
| Linear response theory in dihedral angle space for protein structural change upon ligand binding. | Q47992788 | ||
| Mechanisms by Which Salt Concentration Moderates the Dynamics of Human Serum Transferrin | Q48232454 | ||
| FbpA iron storage and release are governed by periplasmic microenvironments. | Q48248861 | ||
| Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change. | Q51033724 | ||
| Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single microstate. | Q51459096 | ||
| Molecular mechanism investigation of the neutralization of cadmium toxicity by transferrin. | Q51568168 | ||
| Elucidating the structural mechanisms for biological activity of the chemokine family. | Q52066466 | ||
| Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability. | Q53323308 | ||
| The structure of ferrihydrite, a nanocrystalline material. | Q53954369 | ||
| Definition and testing of the GROMOS force-field versions 54A7 and 54B7 | Q56225271 | ||
| Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis | Q56688821 | ||
| ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function | Q56879918 | ||
| Rapid insight into C60 influence on biological functions of proteins | Q57008825 | ||
| A critical evaluation of DFT, including time-dependent DFT, applied to bioinorganic chemistry | Q58010143 | ||
| Non-heme iron through the three domains of life | Q58484036 | ||
| Density Functional Theory Study on Metal-Binding Energies for Human Serum Transferrin-Metal Complexes | Q58689778 | ||
| Atomistic simulations of reactive processes in the gas- and condensed-phase | Q58901084 | ||
| Molecular dynamics simulations of iron- and aluminum-loaded serum transferrin: protonation of Tyr188 is necessary to prompt metal release. | Q42716615 | ||
| Aluminium transport in blood serum. Binding of aluminium by human transferrin in the presence of human albumin and citrate | Q42792470 | ||
| Kinetics and mechanism of exogenous anion exchange in FeFbpA-NTA: significance of periplasmic anion lability and anion binding activity of ferric binding protein A. | Q43265264 | ||
| Dynamic linear response theory for conformational relaxation of proteins | Q43712430 | ||
| Investigation of the mechanism of iron release from the C-lobe of human serum transferrin: mutational analysis of the role of a pH sensitive triad | Q44384174 | ||
| Specificity of the synergistic anion for iron binding by ferric binding protein from Neisseria gonorrhoeae. | Q44974420 | ||
| Structure and Dynamics Study of LeuT Using the Markov State Model and Perturbation Response Scanning Reveals Distinct Ion Induced Conformational States | Q45329990 | ||
| Heme proteins--diversity in structural characteristics, function, and folding | Q45736215 | ||
| Iron and bismuth bound human serum transferrin reveals a partially-opened conformation in the N-lobe | Q27675555 | ||
| Structural basis for iron piracy by pathogenic Neisseria | Q27677223 | ||
| X-ray crystal structure of a recombinant human myoglobin mutant at 2.8 A resolution | Q27684036 | ||
| "Anion clamp" allows flexible protein to impose coordination geometry on metal ions | Q27700147 | ||
| Structural evidence for a pH-sensitive dilysine trigger in the hen ovotransferrin N-lobe: implications for transferrin iron release | Q27731436 | ||
| Structure of the recombinant N-terminal lobe of human lactoferrin at 2.0 A resolution | Q27732002 | ||
| Structure of Haemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily | Q27747119 | ||
| Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release | Q27758031 | ||
| Ligand-induced conformational change in transferrins: crystal structure of the open form of the N-terminal half-molecule of human transferrin | Q27765630 | ||
| Regulation of iron transport and the role of transferrin | Q28253009 | ||
| Structure of the bacterial plant-ferredoxin receptor FusA | Q28314915 | ||
| Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study | Q28367690 | ||
| Unusual Synergism of Transferrin and Citrate in the Regulation of Ti(IV) Speciation, Transport, and Toxicity | Q28394138 | ||
| Development and testing of a general amber force field | Q29547642 | ||
| Atomic-level characterization of the structural dynamics of proteins | Q29616380 | ||
| Metal Ion Modeling Using Classical Mechanics | Q30363020 | ||
| Network-based models as tools hinting at nonevident protein functionality | Q30414102 | ||
| Nutritional immunity. Escape from bacterial iron piracy through rapid evolution of transferrin | Q30653243 | ||
| Benchmark Energetic Data in a Model System for Grubbs II Metathesis Catalysis and Their Use for the Development, Assessment, and Validation of Electronic Structure Methods | Q31028417 | ||
| Simulations of allosteric transitions | Q33350662 | ||
| The SWISS-PROT protein sequence data bank and its new supplement TREMBL | Q33463803 | ||
| The unique kinetics of iron release from transferrin: the role of receptor, lobe-lobe interactions, and salt at endosomal pH | Q33625506 | ||
| Mathematical modeling of the dynamic storage of iron in ferritin | Q33737155 | ||
| Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations | Q33795135 | ||
| Noncanonical interactions between serum transferrin and transferrin receptor evaluated with electrospray ionization mass spectrometry | Q33929235 | ||
| Anisotropy of fluctuation dynamics of proteins with an elastic network model | Q33931550 | ||
| The structural mechanism for iron uptake and release by transferrins | Q34005753 | ||
| Quantum mechanical methods for enzyme kinetics | Q34125125 | ||
| A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein | Q34183823 | ||
| Biomolecular simulation: a computational microscope for molecular biology | Q34266180 | ||
| Chemistry and biology of eukaryotic iron metabolism | Q34317866 | ||
| Unsuspected pathway of the allosteric transition in hemoglobin | Q34804640 | ||
| The influence of the synergistic anion on iron chelation by ferric binding protein, a bacterial transferrin | Q34915001 | ||
| Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water | Q35013396 | ||
| Molecular dynamics simulations of metalloproteins | Q35053362 | ||
| Mechanisms of metalloenzymes studied by quantum chemical methods | Q35087347 | ||
| Identification of a kinetically significant anion binding (KISAB) site in the N-lobe of human serum transferrin | Q35399642 | ||
| Force fields for protein simulations | Q35590728 | ||
| The long history of iron in the Universe and in health and disease | Q35672646 | ||
| Modeling non-heme iron proteins | Q35737607 | ||
| The crystal structure of iron-free human serum transferrin provides insight into inter-lobe communication and receptor binding | Q35850061 | ||
| On the control mechanisms of the nitrite level in Escherichia coli cells: the mathematical model | Q35907918 | ||
| The transferrin-iron import system from pathogenic Neisseria species | Q36309845 | ||
| Modeling heme proteins using atomistic simulations | Q36675200 | ||
| Role of citrate and phosphate anions in the mechanism of iron(III) sequestration by ferric binding protein: kinetic studies of the formation of the holoprotein of wild-type FbpA and its engineered mutants | Q36908340 | ||
| Common dynamics of globin family proteins | Q36911462 | ||
| Protein dynamics explain the allosteric behaviors of hemoglobin | Q37156659 | ||
| Cytoplasmic pH measurement and homeostasis in bacteria and archaea | Q37539166 | ||
| Protein dynamics and ligand migration interplay as studied by computer simulation. | Q37783384 | ||
| Molecular dynamics simulations of protein dynamics and their relevance to drug discovery | Q37802710 | ||
| Kinetics of iron release from transferrin bound to the transferrin receptor at endosomal pH. | Q37893753 | ||
| Anion binding properties of the transferrins. Implications for function | Q37918614 | ||
| FbpA--a bacterial transferrin with more to offer | Q37935982 | ||
| Beyond bilobal: transferrin homologs having unusual domain architectures | Q37943915 | ||
| Local motifs in proteins combine to generate global functional moves | Q38027494 | ||
| Small ligand-globin interactions: reviewing lessons derived from computer simulation. | Q38087453 | ||
| Computational modelling of oxygenation processes in enzymes and biomimetic model complexes | Q38164447 | ||
| Applications of density functional theory to iron-containing molecules of bioinorganic interest | Q38210222 | ||
| New generation of elastic network models | Q38682895 | ||
| Perturbation-Response Scanning Reveals Key Residues for Allosteric Control in Hsp70. | Q38785682 | ||
| Solving Biology's Iron Chemistry Problem with Ferritin Protein Nanocages. | Q38872840 | ||
| Protein effects in non-heme iron enzyme catalysis: insights from multiscale models | Q38882719 | ||
| Understanding the role of dynamics in the iron sulfur cluster molecular machine | Q39635179 | ||
| A quantitative model for oxygen uptake and release in a family of hemeproteins. | Q39788551 | ||
| Iron transport and storage proteins | Q40289294 | ||
| New Benchmark Set of Transition-Metal Coordination Reactions for the Assessment of Density Functionals | Q40297210 | ||
| Dual role of Lys206-Lys296 interaction in human transferrin N-lobe: iron-release trigger and anion-binding site | Q40939313 | ||
| Protonation states of remote residues affect binding-release dynamics of the ligand but not the conformation of apo ferric binding protein | Q41735837 | ||
| Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein | Q41889422 | ||
| Manipulation of Conformational Change in Proteins by Single-Residue Perturbations | Q42108854 | ||
| Sulfate as a synergistic anion facilitating iron binding by the bacterial transferrin FbpA: the origins and effects of anion promiscuity | Q42142890 | ||
| The distribution of iron between the metal-binding sites of transferrin human serum | Q42213003 | ||
| The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions | Q42653614 | ||
| P433 | issue | 11 | |
| P921 | main subject | computational biology | Q177005 |
| P304 | page(s) | 1513-1533 | |
| P577 | publication date | 2017-10-02 | |
| P1433 | published in | Metallomics | Q3307262 |
| P1476 | title | Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins | |
| P478 | volume | 9 |
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