James Allen &ndash; Scholarly Works

2018

Influence of the Electrochemical Properties of the Bacteriochlorophyll Dimer on Triplet Energy-Transfer Dynamics in Bacterial Reaction Centers

Mandal, S., Espiritu, E., Akram, N., Lin, S., Williams, J., Allen, J. & Woodbury, N., Nov 8 2018, In : Journal of Physical Chemistry B. 122, 44, p. 10097-10107 11 p.

Research output: Contribution to journal › Article

Bacteriochlorophylls

Energy Transfer

Electrochemical properties

Dimers

Energy transfer

1 Citation (Scopus)

Remembering George Feher (1924–2017)

Okamura, M. Y., Lubitz, W. & Allen, J., May 25 2018, (Accepted/In press) In : Photosynthesis Research. p. 1-15 15 p.

Research output: Contribution to journal › Article

Photosynthesis

photosynthesis

Photosynthetic Reaction Center Complex Proteins

Proton transfer

autotrophs

2017

Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides

Espiritu, E., Olson, T. L., Williams, J. & Allen, J., Dec 12 2017, In : Biochemistry. 56, 49, p. 6460-6469 10 p.

Research output: Contribution to journal › Article

Rhodobacter sphaeroides

Electrons

Bacteriochlorophylls

Proteins

Dimers

5 Citations (Scopus)

Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins

Olson, T. L., Espiritu, E., Edwardraja, S., Canarie, E., Flores, M., Williams, J., Ghirlanda, G. & Allen, J., Dec 1 2017, In : Biochimica et Biophysica Acta - Bioenergetics. 1858, 12, p. 945-954 10 p.

Research output: Contribution to journal › Article

Proteins

Hydrogen Peroxide

Metals

Electrons

Oxygen

1 Citation (Scopus)

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase

Srivastava, A. P., Hardy, E. P., Allen, J., Vaccaro, B. J., Johnson, M. K. & Knaff, D. B., Oct 17 2017, In : Biochemistry. 56, 41, p. 5582-5592 11 p.

Research output: Contribution to journal › Article

Nitrate Reductase

Ferredoxins

Binding Sites

Electron Spin Resonance Spectroscopy

Computer Simulation

5 Citations (Scopus)

Mechanism of Triplet Energy Transfer in Photosynthetic Bacterial Reaction Centers

Mandal, S., Carey, A. M., Locsin, J., Gao, B. R., Williams, J., Allen, J., Lin, S. & Woodbury, N., Jul 13 2017, In : Journal of Physical Chemistry B. 121, 27, p. 6499-6510 12 p.

Research output: Contribution to journal › Article

Photosynthetic Reaction Center Complex Proteins

carotenoids

Energy Transfer

Carotenoids

Energy transfer

2016

8 Citations (Scopus)

Design of dinuclear manganese cofactors for bacterial reaction centers

Olson, T. L., Espiritu, E., Edwardraja, S., Simmons, C. R., Williams, J., Ghirlanda, G. & Allen, J., May 1 2016, In : Biochimica et Biophysica Acta - Bioenergetics. 1857, 5, p. 539-547 9 p.

Research output: Contribution to journal › Article

Manganese

Proteins

Metals

Electrons

Cytochromes c2

2015

5 Citations (Scopus)

Copper Environment in Artificial Metalloproteins Probed by Electron Paramagnetic Resonance Spectroscopy

Flores, M., Olson, T. L., Wang, D., Edwardraja, S., Shinde, S., Williams, J., Ghirlanda, G. & Allen, J., Oct 29 2015, In : Journal of Physical Chemistry B. 119, 43, p. 13825-13833 9 p.

Research output: Contribution to journal › Article

Metalloproteins

Paramagnetic resonance

Copper

electron paramagnetic resonance

Metals

5 Citations (Scopus)

Identification of Amino Acids at the Catalytic Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase

Srivastava, A. P., Allen, J., Vaccaro, B. J., Hirasawa, M., Alkul, S., Johnson, M. K. & Knaff, D. B., Sep 15 2015, In : Biochemistry. 54, 36, p. 5557-5568 12 p.

Research output: Contribution to journal › Article

Nitrate Reductase

Ferredoxins

Catalytic Domain

Mutagenesis

Electrons

11 Citations (Scopus)

The SMN structure reveals its crucial role in snRNP assembly

Seng, C. O., Magee, C., Young, P. J., Lorson, C. L. & Allen, J., Apr 15 2015, In : Human Molecular Genetics. 24, 8, p. 2138-2146 9 p., ddu734.

Research output: Contribution to journal › Article

Small Nuclear Ribonucleoproteins

Spinal Muscular Atrophy

SMN Complex Proteins

Spliceosomes

RNA Splicing

2014

Electronic structure of the Mn-cofactor of modified bacterial reaction centers measured by electron paramagnetic resonance and electron spin echo envelope modulation spectroscopies

Tufts, A. A., Flores, M., Olson, T. L., Williams, J. & Allen, J., 2014, In : Photosynthesis Research. 120, 1-2, p. 207-220 14 p.

Research output: Contribution to journal › Article

electron paramagnetic resonance spectroscopy

Electron Spin Resonance Spectroscopy

electronics

Electronic structure

Paramagnetic resonance

9 Citations (Scopus)

Interface for light-driven electron transfer by photosynthetic complexes across block copolymer membranes

Kuang, L., Olson, T. L., Lin, S., Flores, M., Jiang, Y., Zheng, W., Williams, J., Allen, J. & Liang, H., Mar 6 2014, In : Journal of Physical Chemistry Letters. 5, 5, p. 787-791 5 p.

Research output: Contribution to journal › Article

Photosynthetic Reaction Center Complex Proteins

block copolymers

Block copolymers

electron transfer

membranes

6 Citations (Scopus)

Purification and biophysical characterization of the CapA membrane protein FTT0807 from francisella tularensis

Martin-Garcia, J. M., Hansen, D., Zook, J., Loskutov, A. V., Robida, M. D., Craciunescu, F. M., Sykes, K. F., Wachter, R., Fromme, P. & Allen, J., Apr 1 2014, In : Biochemistry. 53, 12, p. 1958-1970 13 p.

Research output: Contribution to journal › Article

Francisella tularensis

Purification

Membrane Proteins

Green Fluorescent Proteins

Ionic strength

8 Citations (Scopus)

The three-dimensional structures of bacterial reaction centers

Olson, T. L., Williams, J. & Allen, J., 2014, In : Photosynthesis Research. 120, 1-2, p. 87-98 12 p.

Research output: Contribution to journal › Article

Bacterial Structures

Photosynthesis

photosynthesis

electron transfer

Blastochloris viridis

54 Citations (Scopus)

Water oxidation by a nickel-glycine catalyst

Wang, D., Ghirlanda, G. & Allen, J., Jul 23 2014, In : Journal of the American Chemical Society. 136, 29, p. 10198-10201 4 p.

Research output: Contribution to journal › Article

Molecular oxygen

Nickel

Glycine

Amino acids

Current density

2013

12 Citations (Scopus)

Influence of protein interactions on oxidation/reduction midpoint potentials of cofactors in natural and de novo metalloproteins

Olson, T. L., Williams, J. & Allen, J., 2013, In : Biochimica et Biophysica Acta - Bioenergetics. 1827, 8-9, p. 914-922 9 p.

Research output: Contribution to journal › Article

Metalloproteins

Oxidation-Reduction

Proteins

Redox reactions

Manganese

10 Citations (Scopus)

Roles of four conserved basic amino acids in a ferredoxin-dependent cyanobacterial nitrate reductase

Srivastava, A. P., Hirasawa, M., Bhalla, M., Chung, J. S., Allen, J., Johnson, M. K., Tripathy, J. N., Rubio, L. M., Vaccaro, B., Subramanian, S., Flores, E., Zabet-Moghaddam, M., Stitle, K. & Knaff, D. B., Jun 25 2013, In : Biochemistry. 52, 25, p. 4343-4353 11 p.

Research output: Contribution to journal › Article

Nitrate Reductase

Ferredoxins

Basic Amino Acids

Electrons

Glutamine

2012

14 Citations (Scopus)

Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers

Allen, J., Olson, T. L., Oyala, P., Lee, W. J., Tufts, A. A. & Williams, J., Feb 14 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 7, p. 2314-2318 5 p.

Research output: Contribution to journal › Article

Superoxides

Photosynthetic Reaction Center Complex Proteins

Oxygen

Light

Photosystem II Protein Complex

13 Citations (Scopus)

PH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum

Camara-Artigas, A., Bacarizo, J., Andujar-Sanchez, M., Ortiz-Salmeron, E., Mesa-Valle, C., Cuadri, C., Martin-Garcia, J. M., Martinez-Rodriguez, S., Mazzuca-Sobczuk, T., Ibañez, M. J. & Allen, J., Oct 2012, In : FEBS Journal. 279, 19, p. 3680-3691 12 p.

Research output: Contribution to journal › Article

Porphyridium

Phycoerythrin

Conformations

Chromophores

Rhodophyta

10 Citations (Scopus)

Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum

Tronrud, D. E. & Allen, J., Apr 2012, In : Photosynthesis Research. 112, 1, p. 71-74 4 p.

Research output: Contribution to journal › Article

Pelodictyon phaeum

Bacteriochlorophylls

Carrier concentration

electrons

Electrons

2011

10 Citations (Scopus)

Carotenoid excited-state properties in photosynthetic purple bacterial reaction centers: Effects of the protein environment

Pan, J., Lin, S., Allen, J., Williams, J., Frank, H. A. & Woodbury, N., Jun 2 2011, In : Journal of Physical Chemistry B. 115, 21, p. 7058-7068 11 p.

Research output: Contribution to journal › Article

carotenoids

Carotenoids

Excited states

proteins

Proteins

10 Citations (Scopus)

Energetics for Oxidation of a Bound Manganese Cofactor in Modified Bacterial Reaction Centers

Kálmán, L., Williams, J. & Allen, J., Apr 26 2011, In : Biochemistry. 50, 16, p. 3310-3320 11 p.

Research output: Contribution to journal › Article

Manganese

Oxidation-Reduction

Bicarbonates

Oxidation

Rate constants

8 Citations (Scopus)

Light-induced conformational changes in photosynthetic reaction centers: Impact of detergents and lipids on the electronic structure of the primary electron donor

Deshmukh, S. S., Akhavein, H., Williams, J., Allen, J. & Kálmán, L., Jun 14 2011, In : Biochemistry. 50, 23, p. 5249-5262 14 p.

Research output: Contribution to journal › Article

Photosynthetic Reaction Center Complex Proteins

Detergents

Electronic structure

Electrons

Lipids

13 Citations (Scopus)

Light-induced conformational changes in photosynthetic reaction centers: Dielectric relaxation in the vicinity of the dimer

Deshmukh, S. S., Williams, J., Allen, J. & Kálmán, L., Jan 25 2011, In : Biochemistry. 50, 3, p. 340-348 9 p.

Research output: Contribution to journal › Article

Photosynthetic Reaction Center Complex Proteins

Dielectric relaxation

Lighting

Dimers

Bacteriochlorophylls

11 Citations (Scopus)

Light-Induced Conformational Changes in Photosynthetic Reaction Centers: Redox-Regulated Proton Pathway near the Dimer

Deshmukh, S. S., Williams, J., Allen, J. & Kálmán, L., Apr 26 2011, In : Biochemistry. 50, 16, p. 3321-3331 11 p.

Research output: Contribution to journal › Article

Photosynthetic Reaction Center Complex Proteins

Dimers

Oxidation-Reduction

Protons

Light

22 Citations (Scopus)

The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers

Allen, J. & Williams, J., Jan 2011, In : Photosynthesis Research. 107, 1, p. 59-69 11 p.

Research output: Contribution to journal › Article

Photosystem II Protein Complex

Photosynthesis

photosystem II

photosynthesis

Electrons

26 Citations (Scopus)

The three-dimensional structure of the FMO protein from Pelodictyon phaeum and the implications for energy transfer

Larson, C. R., Seng, C. O., Lauman, L., Matthies, H. J., Wen, J., Blankenship, R. E. & Allen, J., Feb 2011, In : Photosynthesis Research. 107, 2, p. 139-150 12 p.

Research output: Contribution to journal › Article

Pelodictyon phaeum

Energy Transfer

Bacteriochlorophylls

energy transfer

Energy transfer

2 Citations (Scopus)

Thin film voltammetry of wild type and mutant reaction center proteins from photosynthetic bacteria

Zhang, Y., Lafountain, A. M., Magdaong, N., Fuciman, M., Allen, J., Frank, H. A. & Rusling, J. F., Mar 31 2011, In : Journal of Physical Chemistry B. 115, 12, p. 3226-3232 7 p.

Research output: Contribution to journal › Article

Voltammetry

bacteria

Bacteria

proteins

Proteins

4 Citations (Scopus)

Understanding the polymorphic behaviour of a mutant of the -spectrin SH3 domain by means of two 1.1 Å resolution structures

Cámara-Artigas, A., Gavira, J. A., Casares, S., Garcia-Ruiz, J. M., Conejero-Lara, F., Allen, J. & Martinez, J. C., Mar 2011, In : Acta Crystallographica Section D: Biological Crystallography. 67, 3, p. 189-196 8 p.

Research output: Contribution to journal › Article

Spectrin

src Homology Domains

formic acid

Proline

X-Ray Diffraction

2010

2 Citations (Scopus)

Electronic structure of Fe³⁺ at a metal-binding site introduced in modified bacterial reaction centers

Kálmán, L., Flores, M., Williams, J. & Allen, J., 2010, In : Applied Magnetic Resonance. 37, 1, p. 27-37 11 p.

Research output: Contribution to journal › Article

electronic structure

iron

metals

manganese

carbonates

22 Citations (Scopus)

Enzymatic properties of the ferredoxin-dependent nitrite reductase from chlamydomonas reinhardtii. Evidence for hydroxylamine as a late intermediate in ammonia production

Hirasawa, M., Tripathy, J. N., Sommer, F., Somasundaram, R., Chung, J. S., Nestander, M., Kruthiventi, M., Zabet-Moghaddam, M., Johnson, M. K., Merchant, S. S., Allen, J. & Knaff, D. B., Jan 2010, In : Photosynthesis Research. 103, 2, p. 67-77 11 p.

Research output: Contribution to journal › Article

Ferredoxin-Nitrite Reductase

Nitrite Reductases

Chlamydomonas reinhardtii

Ferredoxins

nitrite reductase

21 Citations (Scopus)

The influence of hydrogen bonds on the electronic structure of light-harvesting complexes from photosynthetic bacteria

Uyeda, G., Williams, J., Roman, M., Mattioli, T. A. & Allen, J., Feb 16 2010, In : Biochemistry. 49, 6, p. 1146-1159 14 p.

Research output: Contribution to journal › Article

Photosynthetic Reaction Center Complex Proteins

Electronic structure

Hydrogen

Bacteria

Hydrogen bonds

2 Citations (Scopus)

Three-dimensional structures reveal multiple ADP/ATP binding modes for a synthetic class of artificial proteins

Simmons, C. R., Magee, C. L., Smith, D. A., Lauman, L., Chaput, J. C. & Allen, J., Oct 12 2010, In : Biochemistry. 49, 40, p. 8689-8699 11 p.

Research output: Contribution to journal › Article

Adenosine Diphosphate

Adenosine Triphosphate

Proteins

Catalysis

Synthetic Biology

2009

11 Citations (Scopus)

A synthetic protein selected for ligand binding affinity mediates ATP hydrolysis

Simmons, C. R., Stomel, J. M., McConnell, M. D., Smith, D. A., Watkins, J. L., Allen, J. & Chaput, J. C., Aug 21 2009, In : ACS Chemical Biology. 4, 8, p. 649-658 10 p.

Research output: Contribution to journal › Article

Hydrolysis

Adenosine Triphosphate

Ligands

Proteins

Synthetic Biology

8 Citations (Scopus)

Effect of anions on the binding and oxidation of divalent manganese and iron in modified bacterial reaction centers

Tang, K., Williams, J., Allen, J. & Kálmán, L., 2009, In : Biophysical Journal. 96, 8, p. 3295-3304 10 p.

Research output: Contribution to journal › Article

Manganese

Bicarbonates

Anions

Iron

Metals

17 Citations (Scopus)

Electron transfer in the Rhodobacter sphaeroides reaction center assembled with zinc bacteriochlorophyll

Lin, S., Jaschke, P. R., Wang, H., Paddock, M., Tufts, A., Allen, J., Rosell, F. I., Mauk, A. G., Woodbury, N. & Beatty, J. T., May 26 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 21, p. 8537-8542 6 p.

Research output: Contribution to journal › Article

Bacteriochlorophylls

Rhodobacter sphaeroides

Zinc

Electrons

Photosystem I Protein Complex

10 Citations (Scopus)

EPR, ENDOR, and Special TRIPLE measurements of P^•+ in wild type and modified reaction centers from Rb. sphaeroides

Allen, J., Cordova, J. M., Jolley, C. C., Murray, T. A., Schneider, J. W., Woodbury, N., Williams, J., Niklas, J., Klihm, G., Reus, M. & Lubitz, W., Jan 2009, In : Photosynthesis Research. 99, 1, p. 1-10 10 p.

Research output: Contribution to journal › Article

Electron Spin Resonance Spectroscopy

Paramagnetic resonance

electron paramagnetic resonance spectroscopy

Electrons

Aspartic Acid

6 Citations (Scopus)

Structures of proteins and cofactors: X-ray crystallography

Allen, J., Seng, C. & Larson, C., Nov 2009, In : Photosynthesis Research. 102, 2, p. 231-240 10 p.

Research output: Contribution to journal › Article

X ray crystallography

X Ray Crystallography

protein structure

X-ray diffraction

Proteobacteria

15 Citations (Scopus)

The interaction of spinach nitrite reductase with ferredoxin: A site-directed mutation study

Hirasawa, M., Tripathy, J. N., Somasundaram, R., Johnson, M. K., Bhalla, M., Allen, J. & Knaff, D. B., May 2009, In : Molecular Plant. 2, 3, p. 407-415 9 p.

Research output: Contribution to journal › Article

Ferredoxin-Nitrite Reductase

Ferredoxins

nitrite reductase

ferredoxins

Spinacia oleracea

30 Citations (Scopus)

Unusual temperature dependence of photosynthetic electron transfer due to protein dynamics

Wang, H., Lin, S., Katilius, E., Laser, C., Allen, J., Williams, J. & Woodbury, N., Jan 22 2009, In : Journal of Physical Chemistry B. 113, 3, p. 818-824 7 p.

Research output: Contribution to journal › Article

electron transfer

proteins

Proteins

Conformations

temperature dependence

2008

16 Citations (Scopus)

Comparison of bacterial reaction centers and photosystem II

Kálmán, L., Williams, J. & Allen, J., Oct 2008, In : Photosynthesis Research. 98, 1-3, p. 643-655 13 p.

Research output: Contribution to journal › Article

Photosystem II Protein Complex

photosystem II

electrons

Electrons

protons

2007

3 Citations (Scopus)

Changes in metal specificity due to iron ligand substitutions in reaction centers from Rhodobacter sphaeroides

Williams, J., Paddock, M. L., Way, Y. P. & Allen, J., 2007, In : Applied Magnetic Resonance. 31, 1-2, p. 45-58 14 p.

Research output: Contribution to journal › Article

Substitution reactions

Iron

Metals

substitutes

Ligands

177 Citations (Scopus)

Protein dynamics control the kinetics of initial electron transfer in photosynthesis

Wang, H., Lin, S., Allen, J., Williams, J., Blankert, S., Laser, C. & Woodbury, N., May 4 2007, In : Science. 316, 5825, p. 747-750 4 p.

Research output: Contribution to journal › Article

Photosynthesis

Electrons

Rhodobacter sphaeroides

Proteins

Tryptophan

3 Citations (Scopus)

Reduction of the oxidized bacteriochlorophyll dimer in reaction centers by ferrocene is dependent upon the driving force

Kálmán, L., Haffa, A. L. M., Williams, J., Woodbury, N. & Allen, J., 2007, In : Journal of Porphyrins and Phthalocyanines. 11, 3-4, p. 205-211 7 p.

Research output: Contribution to journal › Article

Bacteriochlorophylls

Dimers

Rate constants

Deprotonation

Biochemistry

15 Citations (Scopus)

Structural insights into the evolution of a non-biological protein: Importance of surface residues in protein fold optimization

Smith, M. D., Rosenow, M. A., Wang, M., Allen, J., Szostak, J. W. & Chaput, J. C., May 23 2007, In : PLoS One. 2, 5, e467.

Research output: Contribution to journal › Article

Membrane Proteins

Proteins

proteins

Mutation

mutation

9 Citations (Scopus)

The role of tryptophan in the ferredoxin-dependent nitrite reductase of spinach

Tripathy, J. N., Hirasawa, M., Kim, S. K., Setterdahl, A. T., Allen, J. & Knaff, D. B., Oct 2007, In : Photosynthesis Research. 94, 1, p. 1-12 12 p.

Research output: Contribution to journal › Article

Ferredoxin-Nitrite Reductase

Nitrite Reductases

Ferredoxins

nitrite reductase

ferredoxins

2006

7 Citations (Scopus)

Crystallization and structural analysis of GADPH from Spinacia oleracea in a new form

Cámara-Artigas, A., Hirasawa, M., Knaff, D. B., Wang, M. & Allen, J., Nov 2006, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 62, 11, p. 1087-1092 6 p.

Research output: Contribution to journal › Article

Spinacia oleracea

Crystallization

structural analysis

Structural analysis

pyridine nucleotides

7 Citations (Scopus)

Iron as a bound secondary electron donor in modified bacterial reaction centers

Kálmán, L., LoBrutto, R., Williams, J. & Allen, J., Nov 21 2006, In : Biochemistry. 45, 46, p. 13869-13874 6 p.

Research output: Contribution to journal › Article

Iron

Electrons

Manganese

Spectrum Analysis

Metals

68 Citations (Scopus)

Structure of phenoxazinone synthase from Streptomyces antibioticus reveals a new type 2 copper center

Smith, A. W., Camara-Artigas, A., Wang, M., Allen, J. & Francisco, W. A., Apr 11 2006, In : Biochemistry. 45, 14, p. 4378-4387 10 p.

Research output: Contribution to journal › Article

Streptomyces antibioticus

Copper

Dactinomycin

Oxidoreductases

Atoms

2005

45 Citations (Scopus)

Design of a redox-linked active metal site: Manganese bound to bacterial reaction centers at a site resembling that of photosystem II

Thielges, M., Uyeda, G., Cámara-Artigas, A., Kálmán, L., Williams, J. & Allen, J., May 24 2005, In : Biochemistry. 44, 20, p. 7389-7394 6 p.

Research output: Contribution to journal › Article

Photosystem II Protein Complex

Manganese

Oxidation-Reduction

Catalytic Domain

Metals