Publications by authors named "Stephen A Mills"

9 Publications

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Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic.

bioRxiv 2020 Dec 4. Epub 2020 Dec 4.

Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
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http://dx.doi.org/10.1101/2020.12.01.406637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724657PMC
December 2020

Virtual Boot Camp: COVID-19 evolution and structural biology.

Biochem Mol Biol Educ 2020 09 14;48(5):511-513. Epub 2020 Aug 14.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.

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http://dx.doi.org/10.1002/bmb.21428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590104PMC
September 2020

Co(II) is not oxidized during turnover in the copper amine oxidase from Hansenula polymorpha.

J Biol Inorg Chem 2019 02 23;24(1):31-37. Epub 2018 Oct 23.

Department of Chemistry and Biochemistry, Miami University, 651 E. High St, Oxford, OH, 45056, USA.

Co(II) substitution into the copper amine oxidases (CAOs) has been an effective tool for evaluating the mechanism of oxygen reduction in these enzymes. However, formation of hydrogen peroxide during turnover raises questions about the relevant oxidation state of the cobalt in these enzymes and, therefore, the interpretation of the activity of the metal-substituted enzyme with respect to its mechanism of action. In this study, Co(II) was incorporated into the CAO from Hansenula polymorpha (HPAO). The effect of hydrogen peroxide on the catalytic activity of cobalt-substituted HPAO was evaluated. Hydrogen peroxide, either generated during turnover or added exogenously, caused a decrease in the activity of the enzyme but did not oxidize Co(II) to Co(III). These results are in strong contrast with results from the CAO from Arthrobacter globiformis (AGAO), where hydrogen peroxide causes an increase in the activity of the enzyme as the Co(II) is oxidized to Co(III). The results of this study with HPAO support previous reports that have shown that this enzyme acts by transferring an electron directly from the reduced TPQ cofactor to dioxygen rather than passing the electron through the bound metal ion. Furthermore, these results provide additional evidence to support the idea that different CAOs use different mechanisms for catalysis.
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http://dx.doi.org/10.1007/s00775-018-1624-yDOI Listing
February 2019

Cobalt substitution supports an inner-sphere electron transfer mechanism for oxygen reduction in pea seedling amine oxidase.

J Biol Inorg Chem 2012 Apr 19;17(4):507-15. Epub 2012 Jan 19.

Department of Chemistry and Biochemistry, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.

Copper amine oxidases (CAOs) are a large family of proteins that use molecular oxygen to oxidize amines to aldehydes with the concomitant production of hydrogen peroxide and ammonia. CAOs utilize two cofactors for this reaction: topaquinone (TPQ) and a Cu(II) ion. Two mechanisms for oxygen reduction have been proposed for these enzymes. In one mechanism (involving inner-sphere electron transfer to O(2)), Cu(II) is reduced by TPQ, forming Cu(I), to which O(2) binds, forming a copper-superoxide complex. In an alternative mechanism (involving outer-sphere electron transfer to O(2)), O(2) is directly reduced by TPQ, without reduction of Cu(II). Substitution of Cu(II) with Co(II) has been used to distinguish between the two mechanisms in several CAOs. Because it is unlikely that Co(II) could be reduced to Co(I) in this environment, an inner-sphere mechanism, as described above, is prevented. We adapted metal replacement methods used for other CAOs to the amine oxidase from pea seedlings (PSAO). Cobalt-substituted PSAO (CoPSAO) displayed nominal catalytic activity: k(cat) is 4.7% of the native k(cat), and K(M) (O(2)) for CoPSAO is substantially (22-fold) higher. The greatly reduced turnover number for CoPSAO suggests that PSAO uses the inner-sphere mechanism, as has been predicted from (18)O isotope effect studies (Mukherjee et al. in J Am Chem Soc 130:9459-9473, 2008), and is catalytically compromised when constrained to operate via outer-sphere electron transfer to O(2). This study, together with previous work, provides strong evidence that CAOs use both proposed mechanisms, but each homolog may prefer one mechanism over the other.
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http://dx.doi.org/10.1007/s00775-011-0872-xDOI Listing
April 2012

Atypia predicting prognosis for intracranial extraventricular neurocytomas.

J Neurosurg 2012 Feb 4;116(2):349-54. Epub 2011 Nov 4.

Department of Neurological Surgery, University of California at San Francisco, California 94143, USA.

Object: The literature, at present, provides limited information about extraventricular neurocytomas (EVNs) and is almost exclusively composed of case reports or small case series. Treatment for EVNs has largely been guided by results from central neurocytoma outcome studies. The authors present an analysis of all reported intracranial EVN cases to establish if tumor histopathological features can substratify EVN into groups with differing prognosis and help guide treatment decisions.

Methods: The authors identified studies reporting histology, treatment modality, and outcomes for patients with intracranial EVN. The rates of recurrence and survival for patients were compared using Kaplan-Meier analysis. Atypical tumors, defined by MIB-1 labeling index exceeding 3% or atypical histological features, were compared with typical tumors, and patients 50 years of age or older were compared with those younger than 50 years of age.

Results: Eighty-five patients met the inclusion criteria, and 27% of them had an atypical histology. Typical EVNs had a better prognosis than atypical EVNs after primary treatment, with a 5-year recurrence rate of 36% compared with 68% (p < 0.001), and a 5-year mortality rate of 4% compared with 44%, respectively (p < 0.001). Age younger 50 years was associated with a better prognosis than age equal to or greater than 50 years, with a 5-year recurrence rate of 33% and 74%, respectively (p < 0.001), and a 5-year mortality rate of 4% and 52%, respectively (p < 0.001). Multivariate analysis demonstrated that atypical EVNs carried significantly increased risk for recurrence (hazard ratio [HR] 4.91, p < 0.001) and death (HR 22.91, p < 0.01). Gross-total resection was superior to subtotal resection (STR) alone in tumor control rates for typical EVNs (95% and 68%, p < 0.05), and there was a trend for adjuvant external-beam radiotherapy to benefit STR. There was suggestion of similar trends in patients with atypical EVNs.

Conclusions: There are at least 2 distinct histological subtypes of EVN, with different prognostic significances. Atypia or MIB-1 labeling index greater than 3% is a significant predictor of poor prognosis for EVNs. Complete resection or more aggressive attempts at providing adjuvant therapy following STR appear to improve the prognosis for patients with EVNs. Although the authors' results are informative, there are limitations to their analysis. Given the relatively modest total number of cases reported, as well as the nature of the disaggregated analysis, the authors were not able to use formal meta-analytical methods to limit the impact of between center heterogeneity. Additionally, they were not able to control for individual differences in data analysis and presentation across the different studies included in their analysis.
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http://dx.doi.org/10.3171/2011.9.JNS10783DOI Listing
February 2012

Structure and activity of CPNGRC: a modified CD13/APN peptidic homing motif.

Chem Biol Drug Des 2010 Jun 30;75(6):551-62. Epub 2010 Mar 30.

Department of Biology, University of San Diego, San Diego, CA 92110, USA.

Asn-Gly-Arg peptides have been designed as vehicles for the delivery of chemotherapeutics, magnetic resonance imaging contrast agents, and fluorescence labels to tumor cells, and cardiac angiogenic tissue. Specificity is derived via an interaction with aminopeptidase N, also known as CD13, a cell surface receptor that is highly expressed in angiogenic tissue. Peptides containing the CNGRC homing sequence tethered to a pro-apoptotic peptide sequence have the ability to specifically induce apoptosis in tumor cells. We have now identified a modification to the Asn-Gly-Arg homing sequence motif that improves overall binding affinity to aminopeptidase N. Through the addition of a proline residue, the new peptide with sequence, CPNGRC, inhibits aminopeptidase N proteolytic activity with an IC(50) of 10 microM, a value that is 30-fold lower than that for CNGRC. Both peptides are cyclized via a disulfide bridge between cysteines. Steady-state kinetic experiments suggest that efficient aminopeptidase N inhibition is achieved through the highly cooperative binding of two molecules of CPNGRC. We have used NMR-derived structural constraints for the elucidation of the solution structures CNGRC and CPNGRC. Resulting structures of CNGRC and CPNGRC have significant differences in the backbone torsion angles, which may contribute to the enhanced binding affinity and demonstrated enzyme inhibition by CPNGRC.
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http://dx.doi.org/10.1111/j.1747-0285.2010.00974.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890305PMC
June 2010

Metal binding characteristics and role of iron oxidation in the ferric uptake regulator from Escherichia coli.

Biochemistry 2005 Oct;44(41):13553-9

Department of Chemistry, University of California, Berkeley, California 94720, USA.

The ferric uptake regulator is a metal-dependent transcription repressor that is activated by divalent transition metal cations. Fe(II) is believed to be the primary functional metal in vivo; however, the ability of other divalent cations to activate Fur brings into question the true physiological metal. Furthermore, the role of different oxidation states of iron in activating Fur has not been determined. Comparison of the affinity of different metals with intracellular metal concentrations would suggest which metals activate Fur in vivo; however, no accurate determinations of the affinity of Fur for metals have been reported. In this study, methods for reconstituting Fur with Fe(II), Fe(III), Co(II), and Zn(II) are described. Reconstituted protein was assayed for DNA affinity by gel shift assays. Fur is activated for DNA binding when reconstituted with Fe(III), as well as Fe(II), Zn(II), Co(II), and Mn(II), with little difference in DNA affinity for the different metallo forms of Fur. The affinity of Fur for the different metals was determined and ranges over several orders of magnitude in the following order: Zn(II) > Co(II) > Fe(II) > Mn(II). Only Fe(II) binds with sufficient affinity to activate Fur significantly at physiological metal concentrations, when compared to previously determined total metal concentrations in Escherichia coli.
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http://dx.doi.org/10.1021/bi0507579DOI Listing
October 2005

Mechanistic comparison of the cobalt-substituted and wild-type copper amine oxidase from Hansenula polymorpha.

Biochemistry 2002 Aug;41(34):10577-84

Department of Chemistry, University of California, Berkeley, CA 94720, USA.

A recent report by Mills and Klinman [Mills, S. A., and Klinman, J. P. (2000) J. Am. Chem. Soc. 122, 9897-9904] described the preparation and initial characterization of a cobalt-substituted form of the copper amine oxidase from Hansenula polymorpha (HPAO). This enzyme was found to be fully catalytically active at saturating substrate concentrations, but with a K(m) for O(2) approximately 70-fold higher than that of the copper-containing, wild-type enzyme. Herein, we report a detailed analysis of the mechanism of catalysis for the wild-type and the cobalt-substituted forms of HPAO. Both forms of enzyme are concluded to utilize the same mechanism for oxygen reduction, involving initial, rate-limiting electron transfer from the reduced cofactor of the enzyme to prebound dioxygen. Superoxide formed in this manner is stabilized by the active site metal, facilitating the transfer of a second electron and two protons to form the product hydrogen peroxide. The elevated K(m) for O(2) at the dioxygen binding site in Co-substituted HPAO, relative to that of wild-type HPAO, is proposed to be due to a change in the net charge at the adjacent metal site from +1 (cupric hydroxide) in wild-type enzyme to +2 (cobaltous H(2)O) in cobalt-substituted HPAO.
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http://dx.doi.org/10.1021/bi0200864DOI Listing
August 2002

Catalytic mechanism of the topa quinone containing copper amine oxidases.

Biochemistry 2002 Jul;41(30):9269-78

Department of Chemistry, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1021/bi020246bDOI Listing
July 2002