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1.
Chemphyschem ; 22(24): 2585-2593, 2021 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-34643979

RESUMO

Benzene bisamides are promising building blocks for supramolecular nano-objects. Their functionality depends on morphology and surface properties. However, a direct link between surface properties and molecular structure itself is missing for this material class. Here, we investigate this interplay for two series of 1,4-benzene bisamides with symmetric and asymmetric peripheral substitution. We elucidated the crystal structures, determined the nano-object morphologies and derived the wetting behaviour of the preferentially exposed surfaces. The crystal structures were solved by combining single-crystal and powder X-ray diffraction, solid-state NMR spectroscopy and computational modelling. Bulky side groups, here t-butyl groups, serve as a structure-directing motif into a packing pattern, which favours the formation of thin platelets. The use of slim peripheral groups on both sides, in our case linear perfluorinated, alkyl chains, self-assemble the benzene bisamides into a second packing pattern which leads to ribbon-like nano-objects. For both packing types, the preferentially exposed surfaces consist of the ends of the peripheral groups. Asymmetric substitution with bulky and slim groups leads to an ordered alternating arrangement of the groups exposed to the surface. This allows the hydrophobicity of the surfaces to be gradually altered. We thus identified two leitmotifs for molecular packings of benzene bisamides providing the missing link between the molecular structure, the anisotropic morphologies and adjustable surface properties of the supramolecular nano-objects.

2.
Q Rev Biophys ; 53: e7, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-32624048

RESUMO

Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific functions. The 20th-century modern synthesis, structural biology, and the central dogma explained the machinery of evolution, and nearly neutral theory explained how selection competes with random fixation dynamics that produce molecular clocks essential e.g. for dating evolutionary histories. However, quantitative proteomics revealed that selection pressures not relating to optimal function play much larger roles than previously thought, acting perhaps most importantly via protein expression levels. This paper first summarizes recent progress in the 21st century toward recovering this universal selection pressure. Then, the paper argues that proteome cost minimization is the dominant, underlying 'non-function' selection pressure controlling most of the evolution of already functionally adapted living systems. A theory of proteome cost minimization is described and argued to have consequences for understanding evolutionary trade-offs, aging, cancer, and neurodegenerative protein-misfolding diseases.


Assuntos
Aminoácidos/química , Conformação Molecular , Dobramento de Proteína , Proteoma , Proteômica/métodos , Trifosfato de Adenosina/química , Animais , Evolução Biológica , Biologia Computacional , Humanos , Cinética , Desnaturação Proteica , Seleção Genética , Solventes/química , Temperatura
3.
Internist (Berl) ; 61(1): 96-101, 2020 Jan.
Artigo em Alemão | MEDLINE | ID: mdl-31705159

RESUMO

A 46-year-old woman presented with recurrent right upper quadrant pain. Abdominal ultrasound revealed an inhomogeneous liver lesion (4â€¯× 7 cm) with complex echotexture. Since further contrast-enhanced imaging tests were inconclusive and lesion integrity remained unclear, a left hemihepatectomy was performed. Histological examination revealed a hepatic epithelioid angiomyolipoma. Hepatic epithelioid angiomyolipoma is a rare, mostly benign, mesenchymal hepatic tumor, composed of smooth muscle cells, adipose tissue, and blood vessels of varying proportions, and its correct diagnosis remains a clinical challenge.


Assuntos
Dor Abdominal/etiologia , Angiomiolipoma , Neoplasias Hepáticas , Dor Abdominal/diagnóstico por imagem , Angiomiolipoma/diagnóstico , Angiomiolipoma/patologia , Angiomiolipoma/cirurgia , Biópsia , Feminino , Hepatectomia , Humanos , Fígado/patologia , Neoplasias Hepáticas/diagnóstico , Neoplasias Hepáticas/patologia , Neoplasias Hepáticas/cirurgia , Imageamento por Ressonância Magnética , Pessoa de Meia-Idade
4.
J Chem Inf Model ; 59(12): 5230-5243, 2019 12 23.
Artigo em Inglês | MEDLINE | ID: mdl-31751128

RESUMO

Genetic variations in the gene encoding the copper-transport protein ATP7B are the primary cause of Wilson's disease. Controversially, clinical prevalence seems much smaller than the prevalence estimated by genetic screening tools, causing fear that many people are undiagnosed, although early diagnosis and treatment is essential. To address this issue, we benchmarked 16 state-of-the-art computational disease-prediction methods against established data of missense ATP7B mutations. Our results show that the quality of the methods varies widely. We show the importance of optimizing the threshold of the methods used to distinguish pathogenic from nonpathogenic mutations against data of clinically confirmed pathogenic and nonpathogenic mutations. We find that most methods use thresholds that predict too many ATP7B mutations to be pathogenic. Thus, our findings explain the current controversy on Wilson's disease prevalence because meta-analysis and text search methods include many computational estimates that lead to higher disease prevalence than clinically observed. As proteins and diseases differ widely, a one-size-fits-all threshold cannot distinguish pathogenic and nonpathogenic mutations efficiently, as shown here. We also show that amino acid changes with small evolutionary substitution probability, mainly due to amino acid volume, are more associated with the disease, implying a pathological effect on the conformational state of the protein, which could affect copper transport or adenosine triphosphate recognition and hydrolysis. These findings may be a first step toward a more quantitative genotype-phenotype relationship of Wilson's disease.


Assuntos
ATPases Transportadoras de Cobre/genética , Degeneração Hepatolenticular/enzimologia , Degeneração Hepatolenticular/genética , Mutação , Sequência de Aminoácidos , ATPases Transportadoras de Cobre/química , ATPases Transportadoras de Cobre/metabolismo , Frequência do Gene , Degeneração Hepatolenticular/patologia , Humanos , Prevalência
5.
Sci Rep ; 8(1): 17285, 2018 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-30470810

RESUMO

Fungal laccases (EC 1.10.3.2) are multi-copper oxidases that oxidize a wide variety of substrates. Despite extensive studies, the molecular basis for their diverse activity is unclear. Notably, there is no current way to rationally predict the activity of a laccase toward a given substrate. Such knowledge would greatly facilitate the rational design of new laccases for technological purposes. We report a study of three datasets of experimental Km values and activities for Trametes versicolor and Cerrena unicolor laccase, using a range of protein modeling techniques. We identify diverse binding modes of the various substrates and confirm an important role of Asp-206 and His-458 (T. versicolor laccase numbering) in guiding substrate recognition. Importantly, we demonstrate that experimental Km values correlate with binding affinities computed by MMGBSA. This confirms the common assumption that the protein-substrate affinity is a major contributor to observed Km. From quantitative structure-activity relations (QSAR) we identify physicochemical properties that correlate with observed Km and activities. In particular, the ionization potential, shape, and binding affinity of the substrate largely determine the enzyme's Km for the particular substrate. Our results suggest that Km is not just a binding constant but also contains features of the enzymatic activity. In addition, we identify QSAR models with only a few descriptors showing that phenolic substrates employ optimal hydrophobic packing to reach the T1 site, but then require additional electronic properties to engage in the subsequent electron transfer. Our results advance our ability to model laccase activity and lend promise to future rational optimization of laccases toward phenolic substrates.


Assuntos
Lacase/química , Lacase/metabolismo , Polyporaceae/enzimologia , Trametes/enzimologia , Sequência de Aminoácidos , Cristalografia por Raios X , Modelos Moleculares , Oxirredução , Conformação Proteica , Relação Quantitativa Estrutura-Atividade , Homologia de Sequência , Especificidade por Substrato
7.
BMC Gastroenterol ; 18(1): 75, 2018 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-29855275

RESUMO

BACKGROUND: Adenocarcinomas or combined adeno-neuroendocrine carcinomas (MANEC) of small bowel usually have a dismal prognosis with limited systemic therapy options. This is the first description of a patient showing a germline-related BRCA1 mutated MANEC of his ileum. The tumor presented a susceptibility to a combined chemotherapy and the PARP1-inhibitor olaparib. CASE PRESENTATION: A 74-year old male patient presented with a metastasized MANEC of his ileum. Due to clinical symptoms his ileum-tumor and the single brain metastasis were removed. We verified the same pathogenic (class 5) BRCA1 mutation in different tumor locations. There was no known personal history of a previous malignant tumor. Nevertheless we identified his BRCA1 mutation as germline-related. A systemic treatment was started including Gemcitabine followed by selective internal radiotherapy (SIRT) to treat liver metastases and in the further course Capecitabine but this treatment finally failed after 9 months and all liver metastases showed progression. The treatment failure was the reason to induce an individualized therapeutic approach using combined chemotherapy of carboplatin, paclitaxel and the Poly (ADP-ribose) polymerase- (PARP)-inhibitor olaparib analogous to the treatment protocol of Oza et al. All liver metastases demonstrated with significant tumor regression after 3 months and could be removed. In his most current follow up from December 2017 (25 months after his primary diagnosis) the patient is in a very good general condition without evidence for further metastases. CONCLUSION: We present first evidence of a therapy susceptible germline-related BRCA1 mutation in small bowel adeno-neuroendocrine carcinoma (MANEC). Our findings offer a personalized treatment option. The germline background was unexpected in a 74-year old man with no previously known tumor burden. We should be aware of the familiar background in tumors of older patients as well.


Assuntos
Adenocarcinoma/tratamento farmacológico , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Proteína BRCA1/genética , Carcinoma Neuroendócrino/tratamento farmacológico , Mutação em Linhagem Germinativa , Neoplasias do Íleo/tratamento farmacológico , Adenocarcinoma/genética , Adenocarcinoma/secundário , Idoso , Neoplasias Encefálicas/secundário , Carboplatina/uso terapêutico , Carcinoma Neuroendócrino/genética , Carcinoma Neuroendócrino/secundário , Humanos , Neoplasias do Íleo/genética , Neoplasias do Íleo/patologia , Neoplasias Hepáticas/secundário , Masculino , Paclitaxel/uso terapêutico , Inibidores de Poli(ADP-Ribose) Polimerases/uso terapêutico
8.
J Phys Chem A ; 122(16): 4208-4217, 2018 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-29630380

RESUMO

Spin crossover (SCO) plays a major role in biochemistry, catalysis, materials, and emerging technologies such as molecular electronics and sensors, and thus accurate prediction and design of SCO systems is of high priority. However, the main tool for this purpose, density functional theory (DFT), is very sensitive to applied methodology. The most abundant SCO systems are Fe(II) and Fe(III) systems. Even with average good agreement, a functional may be significantly more accurate for Fe(II) or Fe(III) systems, preventing balanced study of SCO candidates of both types. The present work investigates DFT's performance for well-known Fe(II) and Fe(III) SCO complexes, using various design types and customized versions of GGA, hybrid, meta-GGA, meta-hybrid, double-hybrid, and long-range-corrected hybrid functionals. We explore the limits of DFT performance and identify proficient Fe(II)-Fe(III)-balanced functionals. We identify and quantify remarkable differences in the DFT description of Fe(II) and Fe(III) systems. Most functionals become more accurate once Hartree-Fock exchange is adjusted to 10-17%, regardless of the type of functionals involved. However, this typically introduces a clear Fe(II)-Fe(III) bias. The most accurate functionals measured by mean absolute errors <10 kJ/mol are CAMB3LYP-17, B3LYP*, and B97-15 with 15-17% Hartree-Fock exchange, closely followed by CAMB3LYP and CAMB3LYP-15, OPBE, rPBE-10, and B3P86-15. While GGA functionals display a small Fe(II)-Fe(III) bias, they are generally inaccurate, except the O exchange functional. Hybrid functionals (including B2PLYP double hybrids and meta hybrids) tend to favor HS too much in Fe(II) vs Fe(III), which is important in many studies where the oxidation state of iron can vary, e.g. rational SCO design and studies of catalytic processes involving iron. The only functional with a combined bias <5 kJ/mol and a decent MAE (15 kJ/mol) is our customized PBE0-12 functional. Alternatively one has to sacrifice Fe(II)-Fe(III) balance to use the best functionals for each group separately. We also investigated the precision (measured as the standard deviation of errors) and show that the target accuracy for iron SCO is 10 kJ/mol for accuracy and 5 kJ/mol for precision, and DFT is probably not going to break this limit in the near future. Importantly, all four types of functional behavior (accurate/precise, accurate/imprecise, inaccurate/precise, inaccurate/imprecise) are observed. More generally, our work illustrates the importance not only of overall accuracy but also of balanced accuracy for systems likely to occur in context.

9.
Langmuir ; 34(12): 3610-3618, 2018 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-29510058

RESUMO

Metalloporphyrins are active sites in metalloproteins and synthetic catalysts. They have also been studied extensively by electrochemistry as well as being prominent targets in electrochemical scanning tunneling microscopy (STM). Previous studies of FePPIX adsorbed on graphite and alkylthiol modified Au electrodes showed a pair of reversible Fe(III/II)PPIX peaks at about -0.41 V (vs NHE) at high solution pH. We recently used iron protoporphyrin IX (FePPIX) as an intercalating probe for long-range electrochemical electron transfer through a G-quadruplex oligonucleotide (DNAzyme); this study disclosed two, rather than a single pair of voltammetric peaks with a new and dominating peak, shifted 200 mV positive relative to the ≈-0.4 V peak. Prompted by this unexpected observation, we report here a study of the voltammetry of FePPIX itself on single-crystal Au(111), (100), and (110) and polycrystalline Au electrode surfaces. In all cases the dominating pair of new Fe(III/II)PPIX redox peaks, shifted positively by more than 200 mV compared to those of previous studies appeared. This observation is supported by density functional theory (DFT) which shows that strong dispersion forces in the FePPIX/Au electronic interaction drive the midpoint potential toward positive values. The FePPIX spin states depend on interaction with the Au(111) interface, converting all the Fe(II)/(III)PPIX species into low-spin states. These results support electrochemical evidence for the nature of the electronic coupling between FePPIX and Au-surfaces, and the electronic states of adsorbate molecules, with a bearing also on recent reports of magnetic FePPIX/Au(111) interactions in ultrahigh vacuum (UHV).

10.
Arq. bras. med. vet. zootec. (Online) ; 69(3): 593-596, jun. 2017. ilus
Artigo em Português | LILACS, VETINDEX | ID: biblio-846892

RESUMO

As doenças pulmonares intersticiais constituem um grupo de doenças difusas do parênquima pulmonar, no qual a fibrose pulmonar intersticial está incluída. Histologicamente, esta se caracteriza por hiperplasia de pneumócitos tipo II, hiperplasia ou hipertrofia de músculo liso e fibrose. Embora a patogenia da fibrose pulmonar intersticial não esteja bem elucidada, devido às semelhanças microscópicas encontradas nos pneumócitos tipo II em felinos e na forma familiar da doença em humanos, acredita-se que haja caráter genético para o seu desenvolvimento. Os sinais clínicos frequentemente relatados incluem desconforto respiratório, cianose, letargia e perda de peso. Devido ao caráter progressivo e à ausência de tratamento específico, a doença apresenta prognóstico desfavorável. Foi atendida uma gata de 12 anos de idade, com histórico de dispneia há 20 dias. Ao exame clínico, o animal apresentou dispneia expiratória restritiva, crepitação à ausculta torácica e foi visualizado padrão intersticial ao exame radiográfico do tórax. A paciente foi submetida à punção com agulha fina de tecido pulmonar e veio a óbito algumas horas após o procedimento, apresentando insuficiência respiratória aguda. No exame histológico do tecido pulmonar, foi verificada a ocorrência de fibrose pulmonar idiopática. O objetivo do presente trabalho é relatar um caso de dispneia expiratória restritiva em um felino doméstico devido à fibrose pulmonar idiopática, já que, segundo o conhecimento dos autores, não há nenhum relato da ocorrência da doença no país.(AU)


Interstitial lung diseases are a group of diffuse parenchymal lung diseases in which interstitial lung fibrosis is included. Histologically, it is characterized by type II pneumocyte hyperplasia, hypertrophy or hyperplasia of smooth tissue and fibrosis. Although the pathogenesis of interstitial lung fibrosis has not been elucidated, due to the microscopic similarities found in type II pneumocytes in cats and familial form of the disease in humans, it is believed that there is a genetic trait for development. The frequently reported clinical signs include respiratory distress, cyanosis, lethargy, and weight loss. Due to the progressive nature and the absence of specific treatment, the disease has a poor prognosis. A 12-year-old cat with dyspnea for 20 days was assisted. The animal underwent fine needle aspiration of lung tissue and died few hours after the procedure, with acute respiratory failure. Upon histological examination of lung tissue, the occurrence of idiopathic pulmonary fibrosis was found. The aim of this study is to report a case of restrictive expiratory dyspnea in a domestic feline due to idiopathic pulmonary fibrosis, because, according to our knowledge, there is no report on the occurrence of the disease in our country.(AU)


Assuntos
Animais , Gatos , Dispneia/veterinária , Fibrose Pulmonar Idiopática/veterinária , Células Epiteliais Alveolares , Doenças Pulmonares Intersticiais/veterinária
11.
Inorg Chem ; 55(6): 2717-27, 2016 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-26913489

RESUMO

Iron complexes are important spin crossover (SCO) systems with vital roles in oxidative metabolism and promising technological potential. The SCO tendency depends on the free energy balance of high- and low-spin states, which again depends on physical effects such as dispersion, relativistic effects, and vibrational entropy. This work studied 30 different iron SCO systems with experimentally known thermochemical data, using 12 different density functionals. Remarkably general entropy-enthalpy compensation across SCO systems was identified (R = 0.82, p = 0.002) that should be considered in rational SCO design. Iron(II) complexes displayed higher ΔH and ΔS values than iron(III) complexes and also less steep compensation effects. First-coordination sphere ΔS values computed from numerical frequencies reproduce most of the experimental entropy and should thus be included when modeling spin-state changes in inorganic chemistry (R = 0.52, p = 3.4 × 10(-3); standard error in TΔS ≈ 4.4 kJ/mol at 298 K vs 16 kJ/mol of total TΔS on average). Zero-point energies favored high-spin states by 9 kJ/mol on average. Interestingly, dispersion effects are surprisingly large for the SCO process (average: 9 kJ/mol, but up to 33 kJ/mol) and favor the more compact low-spin state. Relativistic effects favor low-spin by ∼9 kJ/mol on average, but up to 24 kJ/mol. B3LYP*, TPSSh, B2PLYP, and PW6B95 performed best for the typical calculation scheme that includes ZPE. However, if relativistic and dispersion effects are included, only B3LYP* remained accurate. On average, high-spin was favored by LYP by 11-15 kJ/mol relative to other correlation functionals, and by 4.2 kJ/mol per 1% HF exchange in hybrids. 13% HF exchange was optimal without dispersion, and 15% was optimal with all effects included for these systems.

12.
J Phys Chem A ; 118(34): 7104-17, 2014 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-25116644

RESUMO

Quantum-chemical cluster modeling is challenged in the limit of large, soft systems by the effects of dispersion and solvent, and well as other physical interactions. Adenosylcobalamin (AdoCbl, coenzyme B12), as one of the most complex cofactors in life, constitutes such a challenge. The cleavage of its unique organometallic Co-C bond has inspired multiple studies of this cofactor. This paper reports the fully relaxed potential energy surface of Co-C cleavage of AdoCbl, including for the first time all side-chain interactions with the dissociating Ado group. Various methods and corrections for dispersion, relativistic effects, solvent polarity, basis set superposition error, and thermal and vibrational effects were investigated, totaling more than 550 single-point energies for the large model. The results show immense variability depending on method, including solvation, functional type, and dispersion, challenging the conceived accuracy of methods used for such systems. In particular, B3LYP-D3 seems to severely underestimate the Co-C bond strength, consistent with previous results, and BP86 remains accurate for cobalamins when dispersion interactions are accounted for.


Assuntos
Carbono/química , Cobalto/química , Cobamidas/química , Modelos Químicos , Teoria Quântica , Solventes/química , Temperatura
13.
J Inorg Biochem ; 107(1): 15-24, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22178664

RESUMO

Metallothioneins (MT) are small, metal-binding proteins with diverse functions related to metal ion homeostasis. This paper presents the full 384-388-atom structures of the two native Zn(II)- and the Cd(II)-containing domains of human MT2, optimized with density functional theory. The presented structures are accurate to ~0.03 Å for bond lengths and thus provide new physical insight into the detailed electronic structures of MTs, in particular with accurate accounts of bridging vs. terminal bonds not available from NMR or EXAFS. The MT protein enhances the asymmetry, as compared to the protein-free clusters, causing a hierarchy in binding that most likely allows MTs to transfer ions to multiple targets in vivo. The protein polarization is substantial and occurs primarily via the terminal sulfurs, a key mechanism in providing domain-specific electronic structures. The ß-domain polarizes its smaller cluster less on average, due to its less polarizable, higher negative charge density, as reflected in longer MS bond lengths and smaller bond orders. This may explain why MT2ß is more reactive and dynamic and why MTs have evolved two different-size, asymmetric domains with different metal binding affinities fit for different molecular targets of metal ion transfer.


Assuntos
Simulação por Computador , Metalotioneína/química , Modelos Moleculares , Sequência de Aminoácidos , Cádmio/química , Complexos de Coordenação/química , Cisteína/química , Eletroquímica , Humanos , Dados de Sequência Molecular , Estrutura Terciária de Proteína , Teoria Quântica , Zinco/química
14.
J Inorg Biochem ; 105(10): 1286-92, 2011 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-21855825

RESUMO

Porphyrins are much studied due to their biochemical relevance and many applications. The density functional TPSSh has previously accurately described the energy of close-lying electronic states of transition metal systems such as porphyrins. However, a recent study questioned this conclusion based on calculations of five iron(III) porphines. Here, we compute the geometries of 80 different electronic configurations and the free energies of the most stable configurations with the functionals TPSSh, TPSS, and B3LYP. Zero-point energies and entropy favor high-spin by ~4kJ/mol and 0-10kJ/mol, respectively. When these effects are included, and all electronic configurations are evaluated, TPSSh correctly predicts the spin of all the four difficult phenylporphine cases and is within the lower bound of uncertainty of any known theoretical method for the fifth, iron(III) chloroporphine. Dispersion computed with DFT-D3 favors low-spin by 3-53kJ/mol (TPSSh) or 4-15kJ/mol (B3LYP) due to the attractive r(-6) term and the shorter distances in low-spin. The very large and diverse corrections from TPSS and TPSSh seem less consistent with the similarity of the systems than when calculated from B3LYP. If the functional-specific corrections are used, B3LYP and TPSSh are of equal accuracy, and TPSS is much worse, whereas if the physically reasonable B3LYP-computed dispersion effect is used for all functionals, TPSSh is accurate for all systems. B3LYP is significantly more accurate when dispersion is added, confirming previous results.


Assuntos
Heme/química , Ferro/química , Entropia , Modelos Químicos , Modelos Moleculares , Termodinâmica
15.
Phys Rev Lett ; 103(8): 081801, 2009 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-19792715

RESUMO

Using high statistics samples of charged-current numu interactions, the MiniBooNE [corrected] Collaboration reports a measurement of the single-charged-pion production to quasielastic cross section ratio on mineral oil (CH2), both with and without corrections for hadron reinteractions in the target nucleus. The result is provided as a function of neutrino energy in the range 0.4 GeV

16.
J Am Chem Soc ; 131(34): 12155-71, 2009 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-19663382

RESUMO

We have performed a systematic study of chemically possible peroxo-type intermediates occurring in the non-heme di-iron enzyme class Ia ribonucleotide reductase, using spectroscopically calibrated computational chemistry. Density functional computations of equilibrium structures, Fe-O and O-O stretch frequencies, Mossbauer isomer shifts, absorption spectra, J-coupling constants, electron affinities, and free energies of O(2) and proton or water binding are presented for a series of possible intermediates. The results enable structure-property correlations and a new rationale for the changes in carboxylate conformations occurring during the O(2) reaction of this class of non-heme iron enzymes. Our procedure identifies and characterizes various possible candidates for peroxo intermediates experimentally observed along the ribonucleotide reductase dioxygen activation reaction. The study explores how water or a proton can bind to the di-iron site of ribonucleotide reductase and facilitate changes that affect the electronic structure of the iron sites and activate the site for further reaction. Two potential reaction pathways are presented: one where water adds to Fe1 of the cis-mu-1,2 peroxo intermediate P causing opening of a bridging carboxylate to form intermediate P' that has an increased electron affinity and is activated for proton-coupled electron transfer to form the Fe(III)Fe(IV) intermediate X; and one that is more energetically favorable where the P to P' conversion involves addition of a proton to a terminal carboxylate ligand in the site which increases the electron affinity and triggers electron transfer to form X. Both pathways provide a mechanism for the activation of peroxy intermediates in binuclear non-heme iron enzymes for reactivity. The studies further show that water coordination can induce the conformational changes observed in crystal structures of the met state.


Assuntos
Ferro/metabolismo , Ribonucleotídeo Redutases/química , Ribonucleotídeo Redutases/metabolismo , Absorção , Simulação por Computador , Heme , Hidróxidos/química , Isomerismo , Modelos Moleculares , Conformação Molecular , Oxirredução , Oxigênio/química , Peróxidos/química , Prótons , Espectrofotometria Ultravioleta , Espectroscopia de Mossbauer , Termodinâmica , Vibração , Água/química
17.
J Phys Chem A ; 113(37): 10033-9, 2009 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-19697914

RESUMO

Despite their importance in many chemical processes, the relative energies of spin states of transition metal complexes have so far been haunted by large computational errors. By the use of six functionals, B3LYP, BP86, TPSS, TPSSh, M06, and M06L, this work studies nine complexes (seven with iron and two with cobalt) for which experimental enthalpies of spin crossover are available. It is shown that such enthalpies can be used as quantitative benchmarks of a functional's ability to balance electron correlation in both the involved states. TPSSh achieves an unprecedented mean absolute error of approximately 11 kJ/mol in spin transition energies, with the local functional M06L a distant second (25 kJ/mol). Other tested functionals give mean absolute errors of 40 kJ/mol or more. This work confirms earlier suggestions that 10% exact exchange is near-optimal for describing the electron correlation effects of first-row transition metal systems. Furthermore, it is shown that given an experimental structure of an iron complex, TPSSh can predict the electronic state corresponding to that experimental structure. We recommend this functional as current state-of-the-art for studying spin crossover and relative energies of close-lying electronic configurations in first-row transition metal systems.

18.
J Inorg Biochem ; 102(1): 87-100, 2008 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17723245

RESUMO

This work reports density functional computations of metal-substituted models of biological [Fe3S4] clusters in oxidation states [MFe2S4](+/0/-1) (M=Mn, Fe, Co, Ni, Cu, Zn, and Mo). Geometry optimization with a dielectric screening model is shown to provide a substantial improvement in structure, compared to earlier used standard procedures. The error for average Fe-S bonds decreased from 0.038A to 0.016A with this procedure. Four density functionals were compared, B3LYP, BP86, TPSS, and TPSSh. B3LYP and to a lesser extent TPSSh energies were inconsistent with experiment for the oxidized [Fe3S4]+ cluster. BP86 (and to a slightly lesser extent TPSS) was within expected theoretical and experimental uncertainties for all oxidation states, the only qualitative error being 5kJ/mol in favor of the M(S)=3/2 configuration for the [Fe3S4]+ cluster, so BP86 was used for quantitative results. Computed reorganization energies and reduction potentials point directly towards the [Fe3S4] cluster as the superior choice of electron carrier, with the [ZnFe2S4] cluster a close second. In addition, partially and fully Mo-substituted clusters were investigated and found to have very low reorganization energies but too negative reduction potentials. The results provide a direct rationale why any substitution weakens the cluster as an electron carrier, and thus why the [Fe3S4] composition is optimal in the biological clusters.


Assuntos
Proteínas Ferro-Enxofre/química , Ferro/química , Biologia Computacional , Simulação por Computador , Espectroscopia de Ressonância de Spin Eletrônica , Metais/química , Modelos Químicos , Estrutura Molecular , Oxirredução
19.
Inorg Chem ; 46(21): 8710-6, 2007 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-17880061

RESUMO

This work describes the computation and accurate reproduction of subtle shifts in reduction potentials for two mutants of the iron-sulfur protein Pyrococcus furiosus ferredoxin. The computational models involved only first-sphere ligands and differed with respect to one ligand, either acetate (aspartate), thiolate (cysteine), or methoxide (serine). Standard procedures using vacuum optimization gave qualitatively wrong results and errors up to 0.07 V. Using electrostatically screened geometries and large basis sets for expanding the wave functions gave quantitatively correct results, with errors of only 0.03 V. Correspondingly, only this approach predicted a change in the coordination mode of aspartate (i.e., a carboxylate shift) accompanying the reduction of the wild-type cluster, confirming results from synthetic models and explaining why electrostatic screening is necessary. Hence, the carboxylate shift appears to occur in the proteins from which data were collected. The results represent the most accurate predictions of shifts in reduction potentials for modified proteins, the success in part being due to the similar nature of the three amino acid ligands involved. The predicted carboxylate shift is expected to tune aspartate's degree of electron donation to the cluster's two oxidation states, thus making the reversible redox reaction feasible.


Assuntos
Química/métodos , Ferredoxinas/química , Proteínas Ferro-Enxofre/química , Pyrococcus furiosus/metabolismo , Ácido Aspártico/química , Ácidos Carboxílicos/química , Cristalografia por Raios X , Cisteína/química , Ligantes , Modelos Teóricos , Conformação Molecular , Oxirredução , Reprodutibilidade dos Testes , Software , Temperatura
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