Reviews - 1bz6 mentioned but not cited (1)
- Role of atomic contacts in vibrational energy transfer in myoglobin. Mizuno M, Mizutani Y. Biophys Rev 12 511-518 (2020)
Articles - 1bz6 mentioned but not cited (16)
- The molten globule state is unusually deformable under mechanical force. Elms PJ, Chodera JD, Bustamante C, Marqusee S. Proc Natl Acad Sci U S A 109 3796-3801 (2012)
- vGNM: a better model for understanding the dynamics of proteins in crystals. Song G, Jernigan RL. J Mol Biol 369 880-893 (2007)
- Dehydron: a structurally encoded signal for protein interaction. Fernández A, Scott R. Biophys J 85 1914-1928 (2003)
- Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. Li B, Yang YT, Capra JA, Gerstein MB. PLoS Comput Biol 16 e1008291 (2020)
- Hydrogen atoms in proteins: positions and dynamics. Engler N, Ostermann A, Niimura N, Parak FG. Proc Natl Acad Sci U S A 100 10243-10248 (2003)
- Redox-induced structural dynamics of Fe-heme ligand in myoglobin by X-ray absorption spectroscopy. Della Longa S, Arcovito A, Benfatto M, Congiu-Castellano A, Girasole M, Hazemann JL, Lo Bosco A. Biophys J 85 549-558 (2003)
- The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. Fernández A, Scott R, Berry RS. Proc Natl Acad Sci U S A 101 2823-2827 (2004)
- Low-frequency dynamics of Caldariomyces fumago chloroperoxidase probed by femtosecond coherence spectroscopy. Gruia F, Ionascu D, Kubo M, Ye X, Dawson J, Osborne RL, Sligar SG, Denisov I, Das A, Poulos TL, Terner J, Champion PM. Biochemistry 47 5156-5167 (2008)
- Protein flexibility: coordinate uncertainties and interpretation of structural differences. Rashin AA, Rashin AH, Jernigan RL. Acta Crystallogr D Biol Crystallogr 65 1140-1161 (2009)
- Factors correlating with significant differences between X-ray structures of myoglobin. Rashin AA, Domagalski MJ, Zimmermann MT, Minor W, Chruszcz M, Jernigan RL. Acta Crystallogr D Biol Crystallogr 70 481-491 (2014)
- Analysis of the contribution of the globin and reductase domains to the ligand-binding properties of bacterial haemoglobins. Farrés J, Burckhardt-Herold S, Scherrer J, Frey AD, Kallio PT. Biochem J 407 15-22 (2007)
- Analysis of protein dynamics using local-DME calculations. Wu D, Smith S, Mahan H, Jernigan RL, Zhijun Wu. Int J Bioinform Res Appl 7 146-161 (2011)
- Ultrafast Structural Changes Decomposed from Serial Crystallographic Data. Ren Z. J Phys Chem Lett 10 7148-7163 (2019)
- Protein folding mechanism revealed by single-molecule force spectroscopy experiments. Sun H, Guo Z, Hong H, Yu P, Xue Z, Chen H. Biophys Rep 7 399-412 (2021)
- research-article Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Dieckhaus H, Brocidiacono M, Randolph N, Kuhlman B. bioRxiv 2023.07.27.550881 (2023)
- Water stabilizes an alternate turn conformation in horse heart myoglobin. Bronstein A, Marx A. Sci Rep 13 6094 (2023)
Reviews citing this publication (8)
- Chemical shifts in amino acids, peptides, and proteins: from quantum chemistry to drug design. Oldfield E. Annu Rev Phys Chem 53 349-378 (2002)
- Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Chem Rev 118 10840-11022 (2018)
- Molecular aspects of embryonic hemoglobin function. Brittain T. Mol Aspects Med 23 293-342 (2002)
- Protein dynamics from time resolved UV Raman spectroscopy. Balakrishnan G, Weeks CL, Ibrahim M, Soldatova AV, Spiro TG. Curr Opin Struct Biol 18 623-629 (2008)
- Heme-based sensors: theoretical modeling of heme-ligand-protein interactions. Spiro TG, Jarzecki AA. Curr Opin Chem Biol 5 715-723 (2001)
- Quantum chemical studies of protein structure. Oldfield E. Philos Trans R Soc Lond B Biol Sci 360 1347-1361 (2005)
- Ambidentate H-bonding of NO and O2 in heme proteins. Spiro TG, Soldatova AV. J Inorg Biochem 115 204-210 (2012)
- Local structure and dynamics of hemeproteins by X-ray absorption near edge structure spectroscopy. Arcovito A, della Longa S. J Inorg Biochem 112 93-99 (2012)
Articles citing this publication (108)
- Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. Mackerell AD, Feig M, Brooks CL. J Comput Chem 25 1400-1415 (2004)
- Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD. J Chem Theory Comput 8 3257-3273 (2012)
- Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Barends TR, Foucar L, Ardevol A, Nass K, Aquila A, Botha S, Doak RB, Falahati K, Hartmann E, Hilpert M, Heinz M, Hoffmann MC, Köfinger J, Koglin JE, Kovacsova G, Liang M, Milathianaki D, Lemke HT, Reinstein J, Roome CM, Shoeman RL, Williams GJ, Burghardt I, Hummer G, Boutet S, Schlichting I. Science 350 445-450 (2015)
- 1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. Park SY, Yokoyama T, Shibayama N, Shiro Y, Tame JR. J Mol Biol 360 690-701 (2006)
- NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism. Ma X, Sayed N, Beuve A, van den Akker F. EMBO J 26 578-588 (2007)
- Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering. Cammarata M, Levantino M, Schotte F, Anfinrud PA, Ewald F, Choi J, Cupane A, Wulff M, Ihee H. Nat Methods 5 881-886 (2008)
- Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O2 diffusion to the heme. Milani M, Pesce A, Ouellet Y, Ascenzi P, Guertin M, Bolognesi M. EMBO J 20 3902-3909 (2001)
- Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin. Chu K, Vojtchovský J, McMahon BH, Sweet RM, Berendzen J, Schlichting I. Nature 403 921-923 (2000)
- The structure of murine neuroglobin: Novel pathways for ligand migration and binding. Vallone B, Nienhaus K, Brunori M, Nienhaus GU. Proteins 56 85-92 (2004)
- Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering. Cho HS, Dashdorj N, Schotte F, Graber T, Henning R, Anfinrud P. Proc Natl Acad Sci U S A 107 7281-7286 (2010)
- The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin. Brunori M, Vallone B, Cutruzzola F, Travaglini-Allocatelli C, Berendzen J, Chu K, Sweet RM, Schlichting I. Proc Natl Acad Sci U S A 97 2058-2063 (2000)
- Structural basis of human cytoglobin for ligand binding. Sugimoto H, Makino M, Sawai H, Kawada N, Yoshizato K, Shiro Y. J Mol Biol 339 873-885 (2004)
- Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations. Merchant KA, Noid WG, Akiyama R, Finkelstein IJ, Goun A, McClain BL, Loring RF, Fayer MD. J Am Chem Soc 125 13804-13818 (2003)
- Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. Hummer G, Schotte F, Anfinrud PA. Proc Natl Acad Sci U S A 101 15330-15334 (2004)
- Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Bossa C, Anselmi M, Roccatano D, Amadei A, Vallone B, Brunori M, Di Nola A. Biophys J 86 3855-3862 (2004)
- Picosecond time-resolved X-ray crystallography: probing protein function in real time. Schotte F, Soman J, Olson JS, Wulff M, Anfinrud PA. J Struct Biol 147 235-246 (2004)
- Probing substates in sperm whale myoglobin using high-pressure crystallography. Urayama P, Phillips GN, Gruner SM. Structure 10 51-60 (2002)
- Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. Bossa C, Amadei A, Daidone I, Anselmi M, Vallone B, Brunori M, Di Nola A. Biophys J 89 465-474 (2005)
- Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study. Rovira C, Schulze B, Eichinger M, Evanseck JD, Parrinello M. Biophys J 81 435-445 (2001)
- Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand. Thielges MC, Axup JY, Wong D, Lee HS, Chung JK, Schultz PG, Fayer MD. J Phys Chem B 115 11294-11304 (2011)
- Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy. Finkelstein IJ, Zheng J, Ishikawa H, Kim S, Kwak K, Fayer MD. Phys Chem Chem Phys 9 1533-1549 (2007)
- Long-range reactive dynamics in myoglobin. Sage JT, Durbin SM, Sturhahn W, Wharton DC, Champion PM, Hession P, Sutter J, Alp EE. Phys Rev Lett 86 4966-4969 (2001)
- Spin-dependent mechanism for diatomic ligand binding to heme. Franzen S. Proc Natl Acad Sci U S A 99 16754-16759 (2002)
- Time-resolved absorption and UV resonance Raman spectra reveal stepwise formation of T quaternary contacts in the allosteric pathway of hemoglobin. Balakrishnan G, Case MA, Pevsner A, Zhao X, Tengroth C, McLendon GL, Spiro TG. J Mol Biol 340 843-856 (2004)
- Mapping molecular flexibility of proteins with site-directed spin labeling: a case study of myoglobin. López CJ, Oga S, Hubbell WL. Biochemistry 51 6568-6583 (2012)
- Structural studies of constitutive nitric oxide synthases with diatomic ligands bound. Li H, Igarashi J, Jamal J, Yang W, Poulos TL. J Biol Inorg Chem 11 753-768 (2006)
- Primary protein response after ligand photodissociation in carbonmonoxy myoglobin. Sato A, Gao Y, Kitagawa T, Mizutani Y. Proc Natl Acad Sci U S A 104 9627-9632 (2007)
- Structural analysis of fish versus mammalian hemoglobins: effect of the heme pocket environment on autooxidation and hemin loss. Aranda R, Cai H, Worley CE, Levin EJ, Li R, Olson JS, Phillips GN, Richards MP. Proteins 75 217-230 (2009)
- Haemoglobin polymorphisms affect the oxygen-binding properties in Atlantic cod populations. Andersen O, Wetten OF, De Rosa MC, Andre C, Carelli Alinovi C, Colafranceschi M, Brix O, Colosimo A. Proc Biol Sci 276 833-841 (2009)
- NMR reveals hydrogen bonds between oxygen and distal histidines in oxyhemoglobin. Lukin JA, Simplaceanu V, Zou M, Ho NT, Ho C. Proc Natl Acad Sci U S A 97 10354-10358 (2000)
- Crystal structures of cyanide complexes of P450cam and the oxygenase domain of inducible nitric oxide synthase-structural models of the short-lived oxygen complexes. Fedorov R, Ghosh DK, Schlichting I. Arch Biochem Biophys 409 25-31 (2003)
- Water and ligand entry in myoglobin: assessing the speed and extent of heme pocket hydration after CO photodissociation. Goldbeck RA, Bhaskaran S, Ortega C, Mendoza JL, Olson JS, Soman J, Kliger DS, Esquerra RM. Proc Natl Acad Sci U S A 103 1254-1259 (2006)
- Quantitative analysis of x-ray absorption near edge structure data by a full multiple scattering procedure: the Fe-CO geometry in photolyzed carbonmonoxy-myoglobin single crystal. Della Longa S, Arcovito A, Girasole M, Hazemann JL, Benfatto M. Phys Rev Lett 87 155501 (2001)
- Very high resolution structure of a trematode hemoglobin displaying a TyrB10-TyrE7 heme distal residue pair and high oxygen affinity. Pesce A, Dewilde S, Kiger L, Milani M, Ascenzi P, Marden MC, Van Hauwaert ML, Vanfleteren J, Moens L, Bolognesi M. J Mol Biol 309 1153-1164 (2001)
- First-principles calculations of X-ray absorption spectra at the K-edge of 3d transition metals: an electronic structure analysis of the pre-edge. Cabaret D, Bordage A, Juhin A, Arfaoui M, Gaudry E. Phys Chem Chem Phys 12 5619-5633 (2010)
- Myoglobin cavities provide interior ligand pathway. Teeter MM. Protein Sci 13 313-318 (2004)
- Protein structure refinement using 13C alpha chemical shift tensors. Wylie BJ, Schwieters CD, Oldfield E, Rienstra CM. J Am Chem Soc 131 985-992 (2009)
- Cis-dicarbonyl binding at cobalt and iron porphyrins with saddle-shape conformation. Seufert K, Bocquet ML, Auwärter W, Weber-Bargioni A, Reichert J, Lorente N, Barth JV. Nat Chem 3 114-119 (2011)
- Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Kondrashov DA, Zhang W, Aranda R, Stec B, Phillips GN. Proteins 70 353-362 (2008)
- Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures. Ren Z, Srajer V, Knapp JE, Royer WE. Proc Natl Acad Sci U S A 109 107-112 (2012)
- Heme carbonyls: environmental effects on nu(C-O) and Fe-C/C-O bond length correlations. Silvernail NJ, Roth A, Schulz CE, Noll BC, Scheidt WR. J Am Chem Soc 127 14422-14433 (2005)
- Quantitative vibrational dynamics of iron in carbonyl porphyrins. Leu BM, Silvernail NJ, Zgierski MZ, Wyllie GR, Ellison MK, Scheidt WR, Zhao J, Sturhahn W, Alp EE, Sage JT. Biophys J 92 3764-3783 (2007)
- Spectroscopically and kinetically distinct conformational populations of sol-gel-encapsulated carbonmonoxy myoglobin. A comparison with hemoglobin. Samuni U, Dantsker D, Khan I, Friedman AJ, Peterson E, Friedman JM. J Biol Chem 277 25783-25790 (2002)
- Carbon monoxide poisoning is prevented by the energy costs of conformational changes in gas-binding haemproteins. Antonyuk SV, Rustage N, Petersen CA, Arnst JL, Heyes DJ, Sharma R, Berry NG, Scrutton NS, Eady RR, Andrew CR, Hasnain SS. Proc Natl Acad Sci U S A 108 15780-15785 (2011)
- Differential control of heme reactivity in alpha and beta subunits of hemoglobin: a combined Raman spectroscopic and computational study. Jones EM, Monza E, Balakrishnan G, Blouin GC, Mak PJ, Zhu Q, Kincaid JR, Guallar V, Spiro TG. J Am Chem Soc 136 10325-10339 (2014)
- Hemoglobin site-mutants reveal dynamical role of interhelical H-bonds in the allosteric pathway: time-resolved UV resonance Raman evidence for intra-dimer coupling. Balakrishnan G, Tsai CH, Wu Q, Case MA, Pevsner A, McLendon GL, Ho C, Spiro TG. J Mol Biol 340 857-868 (2004)
- Internal water and microsecond dynamics in myoglobin. Kaieda S, Halle B. J Phys Chem B 117 14676-14687 (2013)
- The kinetics of ligand migration in crystallized myoglobin as revealed by molecular dynamics simulations. Anselmi M, Di Nola A, Amadei A. Biophys J 94 4277-4281 (2008)
- Ultrafast dynamics of myoglobin probed by time-resolved resonance Raman spectroscopy. Mizutani Y, Kitagawa T. Chem Rec 1 258-275 (2001)
- Ambidentate H-bonding by heme-bound NO: structural and spectral effects of -O versus -N H-bonding. Xu C, Thomas GS. J Biol Inorg Chem 13 613-621 (2008)
- Angular dependence of dipole-dipole-Curie-spin cross-correlation effects in high-spin and low-spin paramagnetic myoglobin. Pintacuda G, Hohenthanner K, Otting G, Müller N. J Biomol NMR 27 115-132 (2003)
- Characterization of the heme-histidine cross-link in cyanobacterial hemoglobins from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002. Vu BC, Vuletich DA, Kuriakose SA, Falzone CJ, Lecomte JT. J Biol Inorg Chem 9 183-194 (2004)
- Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations. Zahran ZN, Chooback L, Copeland DM, West AH, Richter-Addo GB. J Inorg Biochem 102 216-233 (2008)
- Iron porphyrin carbenes as catalytic intermediates: structures, Mössbauer and NMR spectroscopic properties, and bonding. Khade RL, Fan W, Ling Y, Yang L, Oldfield E, Zhang Y. Angew Chem Int Ed Engl 53 7574-7578 (2014)
- Observation of the cascaded atomic-to-global length scales driving protein motion. Armstrong MR, Ogilvie JP, Cowan ML, Nagy AM, Miller RJ. Proc Natl Acad Sci U S A 100 4990-4994 (2003)
- Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution. Zhang D, Lazim R. Sci Rep 7 44651 (2017)
- Heme reactivity is uncoupled from quaternary structure in gel-encapsulated hemoglobin: a resonance Raman spectroscopic study. Jones EM, Balakrishnan G, Spiro TG. J Am Chem Soc 134 3461-3471 (2012)
- Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins. Kruglik SG, Yoo BK, Franzen S, Vos MH, Martin JL, Negrerie M. Proc Natl Acad Sci U S A 107 13678-13683 (2010)
- Reaction of Aplysia limacina metmyoglobin with hydrogen peroxide. Svistunenko DA, Reeder BJ, Wankasi MM, Silaghi-Dumitrescu RL, Cooper CE, Rinaldo S, Cutruzzolà F, Wilson MT. Dalton Trans 840-850 (2007)
- Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry. Ryde U. Dalton Trans 607-625 (2007)
- Crystal structure of the carbon monoxide complex of human cytoglobin. Makino M, Sawai H, Shiro Y, Sugimoto H. Proteins 79 1143-1153 (2011)
- Iron porphyrins with different imidazole ligands. A theoretical comparative study. Liao MS, Huang MJ, Watts JD. J Phys Chem A 114 9554-9569 (2010)
- Letter The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure. Strickland N, Mulholland AJ, Harvey JN. Biophys J 90 L27-9 (2006)
- Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy. Lima FA, Penfold TJ, van der Veen RM, Reinhard M, Abela R, Tavernelli I, Rothlisberger U, Benfatto M, Milne CJ, Chergui M. Phys Chem Chem Phys 16 1617-1631 (2014)
- Quantifying the importance of protein conformation on ligand migration in myoglobin. Plattner N, Meuwly M. Biophys J 102 333-341 (2012)
- Time-resolved resonance Raman study on ultrafast structural relaxation and vibrational cooling of photodissociated carbonmonoxy myoglobin. Kitagawa T, Haruta N, Mizutani Y. Biopolymers 67 207-213 (2002)
- Electronic structure and dynamics of nitrosyl porphyrins. Scheidt WR, Barabanschikov A, Pavlik JW, Silvernail NJ, Sage JT. Inorg Chem 49 6240-6252 (2010)
- Light-induced relaxation of photolyzed carbonmonoxy myoglobin: a temperature-dependent x-ray absorption near-edge structure (XANES) study. Arcovito A, Lamb DC, Nienhaus GU, Hazemann JL, Benfatto M, Della Longa S. Biophys J 88 2954-2964 (2005)
- QM/MM vibrational mode tracking. Herrmann C, Neugebauer J, Reiher M. J Comput Chem 29 2460-2470 (2008)
- Theoretical characterization of carbon monoxide vibrational spectrum in sperm whale myoglobin distal pocket. Anselmi M, Aschi M, Di Nola A, Amadei A. Biophys J 92 3442-3447 (2007)
- 5-Aminolevulinic acid regulates the immune response in LPS-stimulated RAW 264.7 macrophages. Sugiyama Y, Hiraiwa Y, Hagiya Y, Nakajima M, Tanaka T, Ogura SI. BMC Immunol 19 41 (2018)
- Coupling of protein relaxation to ligand binding and migration in myoglobin. Agmon N. Biophys J 87 1537-1543 (2004)
- Resilience of the iron environment in heme proteins. Leu BM, Zhang Y, Bu L, Straub JE, Zhao J, Sturhahn W, Alp EE, Sage JT. Biophys J 95 5874-5889 (2008)
- Efficient mapping of ligand migration channel networks in dynamic proteins. Lin TL, Song G. Proteins 79 2475-2490 (2011)
- Observation of α-Helical Hydrogen-Bond Cooperativity in an Intact Protein. Li J, Wang Y, Chen J, Liu Z, Bax A, Yao L. J Am Chem Soc 138 1824-1827 (2016)
- Strong ligand-protein interactions revealed by ultrafast infrared spectroscopy of CO in the heme pocket of the oxygen sensor FixL. Nuernberger P, Lee KF, Bonvalet A, Bouzhir-Sima L, Lambry JC, Liebl U, Joffre M, Vos MH. J Am Chem Soc 133 17110-17113 (2011)
- The effect of point mutation on the equilibrium structural fluctuations of ferric Myoglobin. Adamczyk K, Candelaresi M, Kania R, Robb K, Bellota-Antón C, Greetham GM, Pollard MR, Towrie M, Parker AW, Hoskisson PA, Tucker NP, Hunt NT. Phys Chem Chem Phys 14 7411-7419 (2012)
- Conformational fluctuations and electronic properties in myoglobin. Aschi M, Zazza C, Spezia R, Bossa C, Di Nola A, Paci M, Amadei A. J Comput Chem 25 974-984 (2004)
- Unfolding simulations of holomyoglobin from four mammals: identification of intermediates and β-sheet formation from partially unfolded states. Dasmeh P, Kepp KP. PLoS One 8 e80308 (2013)
- α-Hemoglobin-stabilizing protein (AHSP) perturbs the proximal heme pocket of oxy-α-hemoglobin and weakens the iron-oxygen bond. Dickson CF, Rich AM, D'Avigdor WM, Collins DA, Lowry JA, Mollan TL, Khandros E, Olson JS, Weiss MJ, Mackay JP, Lay PA, Gell DA. J Biol Chem 288 19986-20001 (2013)
- Disentangling ligand migration and heme pocket relaxation in cytochrome P450cam. Tetreau C, Mouawad L, Murail S, Duchambon P, Blouquit Y, Lavalette D. Biophys J 88 1250-1263 (2005)
- Protein collective motions coupled to ligand migration in myoglobin. Nishihara Y, Kato S, Hayashi S. Biophys J 98 1649-1657 (2010)
- Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study. Liao MS, Huang MJ, Watts JD. J Phys Chem B 117 10103-10114 (2013)
- Protein relaxation in the photodissociation of myoglobin-CO complexes. Angeloni L, Feis A. Photochem Photobiol Sci 2 730-740 (2003)
- True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Borshchevskiy V, Kovalev K, Round E, Efremov R, Astashkin R, Bourenkov G, Bratanov D, Balandin T, Chizhov I, Baeken C, Gushchin I, Kuzmin A, Alekseev A, Rogachev A, Willbold D, Engelhard M, Bamberg E, Büldt G, Gordeliy V. Nat Struct Mol Biol 29 440-450 (2022)
- Volume and enthalpy profiles of CO rebinding to horse heart myoglobin. Miksovská J, Day JH, Larsen RW. J Biol Inorg Chem 8 621-625 (2003)
- FeP(Im)-AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O(2)). Liao MS, Huang MJ, Watts JD. Mol Phys 109 2035-2048 (2011)
- A Model for Allosteric Communication in Drug Transport by the AcrAB-TolC Tripartite Efflux Pump. Webber A, Ratnaweera M, Harris A, Luisi BF, Ntsogo Enguéné VY. Antibiotics (Basel) 11 52 (2022)
- Design of an infrared laser pulse to control the multiphoton dissociation of the Fe-CO bond in CO-heme compounds. Sharma S, Singh H, Harvey JN, Balint-Kurti GG. J Chem Phys 133 174103 (2010)
- Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model. Zhang Y, Fujisaki H, Straub JE. J Chem Phys 130 025102 (2009)
- Molecular dynamics simulation of carboxy and deoxy human cytoglobin in solution. Zhang B, Xu J, Li Y, Du W, Fang W. J Inorg Biochem 105 949-956 (2011)
- The Fe-heme structure of met-indoleamine 2,3-dioxygenase-2 determined by X-ray absorption fine structure. Aitken JB, Austin CJ, Hunt NH, Ball HJ, Lay PA. Biochem Biophys Res Commun 450 25-29 (2014)
- Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies. Liao MS, Huang MJ, Watts JD. J Mol Model 19 3307-3323 (2013)
- Ultrafast Structural Fluctuations of Myoglobin-Bound Thiocyanate and Selenocyanate Ions Measured with Two-Dimensional Infrared Photon Echo Spectroscopy. Maj M, Kwak K, Cho M. Chemphyschem 16 3468-3476 (2015)
- Vibrational Dynamics of Biological Molecules: Multi-quantum Contributions. Leu BM, Timothy Sage J, Zgierski MZ, Wyllie GR, Ellison MK, Robert Scheidt W, Sturhahn W, Ercan Alp E, Durbin SM. J Phys Chem Solids 66 2250-2256 (2005)
- Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. II. The nu(4) and nu(7) modes of iron-protoporphyrin IX and iron porphine. Zhang Y, Straub JE. J Chem Phys 130 095102 (2009)
- Linear scaling approaches to quantum macromolecular similarity: evaluating the similarity function. Constans P. J Comput Chem 23 1305-1313 (2002)
- pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera). Kuwada T, Hasegawa T, Takagi T, Sato I, Shishikura F. Acta Crystallogr D Biol Crystallogr 66 258-267 (2010)
- Exploring the Strength of the H-Bond in Synthetic Models for Heme Proteins: The Importance of the N-H Acidity of the Distal Base. Alberti MN, Polyhach Y, Tzirakis MD, Tödtli L, Jeschke G, Diederich F. Chemistry 22 10194-10202 (2016)
- High resolution crystal structures of the Cerebratulus lacteus mini-Hb in the unligated and carbomonoxy states. Germani F, Pesce A, Venturini A, Moens L, Bolognesi M, Dewilde S, Nardini M. Int J Mol Sci 13 8025-8037 (2012)
- Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure. Takayanagi M, Kurisaki I, Nagaoka M. Sci Rep 4 4601 (2014)
- The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations. Anselmi M, Di Nola A, Amadei A. Proteins 79 867-879 (2011)
- Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The nu(4) and nu(7) modes of nonplanar nickel porphyrin models. Zhang Y, Straub JE. J Chem Phys 130 215101 (2009)
- Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin. Chillemi G, Anselmi M, Sanna N, Padrin C, Balducci L, Cammarata M, Pace E, Chergui M, Benfatto M. Struct Dyn 5 054101 (2018)
- Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study. Liao MS, Huang MJ, Watts JD. J Inorg Biochem 118 28-38 (2013)
- Integral equation models for solvent in macromolecular crystals. Gray JG, Giambaşu GM, Case DA, Luchko T. J Chem Phys 156 014801 (2022)
- Probing Adaptation of Hydration and Protein Dynamics to Temperature. Doan LC, Dahanayake JN, Mitchell-Koch KR, Singh AK, Vinh NQ. ACS Omega 7 22020-22031 (2022)
- Studies on the binding of CO to low-spin [Fe(II)(Por)L2] complexes: an aid to understanding the binding of CO to haemoglobin and myoglobin. Silver J, Al-Jaff G, Taies JA, Wilson MT, den Engelsen D, Fern GR, Ireland TG. J Biol Inorg Chem 28 65-84 (2023)