Multielectron redox reactions often require multicofactor metalloenzymes to facilitate coupled electron and proton movement, but it is challenging to design artificial enzymes to catalyze these ...important reactions, owing to their structural and functional complexity. We report a designed heteronuclear heme-4Fe-4S cofactor in cytochrome
peroxidase as a structural and functional model of the enzyme sulfite reductase. The initial model exhibits spectroscopic and ligand-binding properties of the native enzyme, and sulfite reduction activity was improved-through rational tuning of the secondary sphere interactions around the 4Fe-4S and the substrate-binding sites-to be close to that of the native enzyme. By offering insight into the requirements for a demanding six-electron, seven-proton reaction that has so far eluded synthetic catalysts, this study provides strategies for designing highly functional multicofactor artificial enzymes.
► A decreasing trend was found in annual precipitation at about 60% of the stations. ► The significant negative trends occurred mostly in the northwest of Iran. ► The strongest negative trend of the ...seasonal series was detected in winter.
Precipitation is a principal element of the hydrological cycle and its temporal variability is important from both the scientific and practical point of view. The annual and seasonal precipitation trends of 41 stations in Iran for the period 1966–2005 have been analyzed using the Mann–Kendall test, the Sen’s slope estimator and the linear regression. The effective sample size method was applied to eliminate the effect of serial correlation on the Mann–Kendall test. The results indicated a decreasing trend in annual precipitation at about 60% of the stations. The decreasing trends were significant at seven stations at the 95% and 99% confidence levels. The magnitude of the significant negative trends in annual precipitation varied from (−)1.999
mm/year at Zanjan station to (−)4.261
mm/year at Sanandaj station. The spatial distribution of the annual precipitation trends showed that the significant negative trends occurred mostly in the northwest of Iran. On the seasonal scale, the trends in the spring and winter precipitations time series were mostly negative. The highest numbers of stations with significant trends occurred in winter while no significant positive or negative trends were detected by the trend tests in autumn precipitation. The significant negative trends ranged between (−)0.283
mm/year at Zahedan station and (−)0.807
mm/year at Sanandaj station in winter season. In addition, the highest and lowest significant increases of precipitation values were obtained over Semnan and Mashhad in summer at the rates of (+)0.110
mm/year and (+)0.036
mm/year, respectively.
Liu et al investigate metalloproteins with cytochrome, iron-sulfur and copper redox centers and present an overview of the redox attributes of designed 6-coordinate heme proteins which imitate ...electron transfer cytochromes. The hemoprotein is present both in the inner mitochondrial membrane of eukaryotes and in Gram-positive and Gram-negative bacteria.
Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned ...by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with L-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L- and D-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.
Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, ...we develop a computational "anchor extension" methodology for targeting protein interfaces by extending a peptide chain around a non-canonical amino acid residue anchor. To test our approach using a well characterized model system, we design cyclic peptides that inhibit histone deacetylases 2 and 6 (HDAC2 and HDAC6) with enhanced potency compared to the original anchor (IC
values of 9.1 and 4.4 nM for the best binders compared to 5.4 and 0.6 µM for the anchor, respectively). The HDAC6 inhibitor is among the most potent reported so far. These results highlight the potential for de novo design of high-affinity protein-peptide interfaces, as well as the challenges that remain.
▶ A significant trend was observed in the annual ET
o series in most of the stations. ▶ The main cause of the increasing trend in ET
o was an increase in air temperature. ▶ The greatest significant ...trends in the seasonal ET
o series were observed in winter. ▶ The greatest significant trends in the monthly ET
o series were found in February.
Reference evapotranspiration (ET
o) is an important element of the hydrological cycle, and changes in ET
o are of great significance for agricultural water use planning, irrigation system design and management. In this study, annual, seasonal and monthly trends in the Penman–Monteith ET
o at 20 meteorological stations during 1966–2005 in the western half of Iran were examined using the Mann–Kendall test, the Sen's slope estimator and the linear regression. Annual analysis of the ET
o series indicated a positive trend in 70% of the stations according to the Mann–Kendall test and the Sen's slope estimator and in 75% of the stations according to the linear regression. The magnitude of significant positive trends in annual ET
o varied from (+)11.28 to (+)2.30
mm/year. On the seasonal scale, stronger increasing trends were identified in ET
o data in winter and summer compared with those in autumn and spring. Meanwhile, the highest numbers of stations with significant trends were found in the monthly ET
o series in February, while the lowest numbers of stations with significant trends were observed in November. Analysis of the impact of climatic variables on the significant increasing trend in ET
o showed that the increasing trend was mainly caused by a significant increase in air temperature during the study period.
In this study, the trends of the annual, seasonal and monthly maximum (T max) and minimum (T min) air temperatures time series were investigated for 20 stations in the western half of Iran during ...1966-2005. Three statistical tests including Mann-Kendall, Sen's slope estimator and linear regression were used for the analysis. The annual T max and T min series showed a positive trend in 85% of the stations and a negative trend in 15% of the stations in the study region. The highest increase of T max and T min values were obtained over Kermanshah and Ahwaz at the rates of (+)0.597°C/decade and (+)0.911°C/decade, respectively. On the seasonal scale, the strongest increasing trends were identified in T max and T min data in summer. The highest numbers of stations with positive significant trends occurred in the monthly T max and T min series in August. In contrast, the lowest numbers of stations with significant positive trends were observed between November and March. Overall, the results showed similar increasing trends for the study variables, although T min generally increased at a higher rate than T max in the study period.
The reduction potential (Eo′) is a critical parameter in determining the efficiency of most biological and chemical reactions. Biology employs three classes of metalloproteins to cover the majority ...of the 2-V range of physiological Eo′s. An ultimate test of our understanding of Eo′ is to find out the minimal number of proteins and their variants that can cover this entire range and the structural features responsible for the extreme Eo′. We report herein the design of the protein azurin to cover a range from +970 mV to −954 mV vs. standard hydrogen electrode (SHE) by mutating only five residues and using two metal ions. Spectroscopic methods have revealed geometric parameters important for the high Eo′. The knowledge gained and the resulting water-soluble redox agents with predictable Eo′s, in the same scaffold with the same surface properties, will find wide applications in chemical, biochemical, biophysical, and biotechnological fields.
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one ...needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron–sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics — the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
While a conserved tyrosine (Tyr) is found in oxidases, the roles of phenol ring pK a and reduction potential in O2 reduction have not been defined despite many years of research on numerous oxidases ...and their models. These issues represent major challenges in our understanding of O2 reduction mechanism in bioenergetics. Through genetic incorporation of unnatural amino acid analogs of Tyr, with progressively decreasing pK a of the phenol ring and increasing reduction potential, in the active site of a functional model of oxidase in myoglobin, a linear dependence of both the O2 reduction activity and the fraction of H2O formation with the pK a of the phenol ring has been established. By using these unnatural amino acids as spectroscopic probe, we have provided conclusive evidence for the location of a Tyr radical generated during reaction with H2O2, by the distinctive hyperfine splitting patterns of the halogenated tyrosines and one of its deuterated derivatives incorporated at the 33 position of the protein. These results demonstrate for the first time that enhancing the proton donation ability of the Tyr enhances the oxidase activity, allowing the Tyr analogs to augment enzymatic activity beyond that of natural Tyr.
![A designed heme-[4Fe-4S] me...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/0036-8075/small "A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme")
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