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Kanai Y, Harada A, Shibata T, Nishimura R, Namiki K, Watanabe M, Nakamura S, Yumoto F, Senda T, Suzuki A, Neya S, Yamamoto Y. Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor. Biochemistry 2017; 56:4500-4508. [DOI: 10.1021/acs.biochem.7b00457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Kanai
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ayaka Harada
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tomokazu Shibata
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kosuke Namiki
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Miho Watanabe
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shunpei Nakamura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Fumiaki Yumoto
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department
of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life
Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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Berry RE, Muthu D, Yang F, Walker FA. NMR studies of the dynamics of high-spin nitrophorins: comparative studies of NP4 and NP2 at close to physiological pH. Biochemistry 2015; 54:221-39. [PMID: 25486224 PMCID: PMC4303294 DOI: 10.1021/bi501305a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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The
β-barrel nitrophorin (NP) heme proteins are found in
the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary
glands. NO is bound to iron of the NPs and is released by dilution
and an increase in pH when the insect spits its saliva into the tissues
of a victim, to aid in obtaining a blood meal. In the adult insect,
there are four nitrophorins, NP1–NP4, which have sequence similarities
in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical).
The available crystal structures of NP4 have been used to propose
that pH-dependent changes in the conformation of two loops between
adjacent β-strands at the front opening of the protein, the
A–B and G–H loops, determine the rate of NO release.
At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this
work, the aqua complexes of NP4 and NP2 have been investigated by
nuclear magnetic resonance (NMR) relaxation measurements to probe
the pico- to nanosecond and micro- to millisecond time scale motions
at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics
at pH 6.5; at pH 7.3, much more dynamics of the loops and most of
the β-strands are observed while the α-helices remain
fairly rigid. In comparison, NP2-OH2 shows much less dynamics,
albeit somewhat more than that of the previously reported NP2-NO complex
[Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910–7925]. The reasons for this
major difference between NP4 and NP2 are discussed.
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Affiliation(s)
- Robert E Berry
- Department of Chemistry and Biochemistry, The University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721-0041, United States
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Berry RE, Yang F, Shokhireva TK, Amoia AM, Garrett S, Goren AM, Korte SR, Zhang H, Weichsel A, Montfort WR, Walker FA. Dimerization of nitrophorin 4 at low pH and comparison to the K1A mutant of nitrophorin 1. Biochemistry 2015; 54:208-20. [PMID: 25489673 PMCID: PMC4303305 DOI: 10.1021/bi5013047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/08/2014] [Indexed: 11/28/2022]
Abstract
Nitrophorin 4, one of the four NO-carrying heme proteins from the salivary glands of Rhodnius prolixus, forms a homodimer at pH 5.0 with a Kd of ∼8 μM. This dimer begins to dissociate at pH 5.5 and is completely dissociated to monomer at pH 7.3, even at 3.7 mM. The dimer is significantly stabilized by binding NO to the heme and at pH 7.3 would require dilution to well below 0.2 mM to completely dissociate the NP4-NO homodimer. The primary techniques used for investigating the homodimer and the monomer-dimer equilibrium were size-exclusion fast protein liquid chromatography at pH 5.0 and (1)H{(15)N} heteronuclear single-quantum coherence spectroscopy as a function of pH and concentration. Preparation of site-directed mutants of NP4 (A1K, D30A, D30N, V36A/D129A/L130A, K38A, R39A, K125A, K125E, D132A, L133V, and K38Q/R39Q/K125Q) showed that the N-terminus, D30, D129, D132, at least one heme propionate, and, by association, likely also E32 and D35 are involved in the dimerization. The "closed loop" form of the A-B and G-H flexible loops of monomeric NP4, which predominates in crystal structures of the monomeric protein reported at pH 5.6 but not at pH 7.5 and which involves all of the residues listed above except D132, is required for dimer formation. Wild-type NP1 does not form a homodimer, but NP1(K1A) and native N-terminal NP1 form dimers in the presence of NO. The homodimer of NP1, however, is considerably less stable than that of NP4 in the absence of NO. This suggests that additional aspartate or glutamate residues present in the C-terminal region of NP4, but not NP1, are also involved in stabilizing the dimer.
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Affiliation(s)
| | - Fei Yang
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - Tatiana K. Shokhireva
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - Angela M. Amoia
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - Sarah
A. Garrett
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - Allena M. Goren
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - Stephanie R. Korte
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - Hongjun Zhang
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - Andrzej Weichsel
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - William R. Montfort
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
| | - F. Ann Walker
- Department of Chemistry and
Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, United States
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Muthu D, Berry RE, Zhang H, Walker FA. NMR studies of the dynamics of nitrophorin 2 bound to nitric oxide. Biochemistry 2013; 52:7910-25. [PMID: 24116947 PMCID: PMC3947638 DOI: 10.1021/bi4010396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Rhodnius nitrophorins are β-barrel proteins of the lipocalin fold with a heme protruding from the open end of the barrel. They are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands, where NO is bound to iron. NO is released by dilution and an increase in pH when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect, there are four nitrophorins, NP1-NP4. At pH 7.3, NP4 releases NO 17 times faster than NP2 does, as measured by stopped-flow kinetics. A number of crystal structures of the least abundant protein, NP4, are available. These structures have been used to propose that two loops between adjacent β-strands at the front opening of the protein, the A-B and G-H loops, determine the rate of NO release. To learn how the protein loops contribute to the release of NO for each of the nitrophorins, the dynamics of these proteins are being studied in our laboratory. In this work, the NP2-NO complex has been investigated by nuclear magnetic resonance relaxation measurements to probe the picosecond-to-nanosecond and microsecond-to-millisecond time scale motions at three pH values, 5.0, 6.5, and 7.3. It is found that at pH 5.0 and 6.5, the NP2-NO complex is rigid and only a few residues in the loop regions show dynamics, while at pH 7.3, somewhat more dynamics, particularly of the A-B loop, are observed. Comparison to other lipocalins shows that all are relatively rigid, and that the dynamics of lipocalins in general are much more subtle than those of mainly α-helical proteins.
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Affiliation(s)
- Dhanasekaran Muthu
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Boulevard, Tucson, AZ 85721-0041
| | - Robert E. Berry
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Boulevard, Tucson, AZ 85721-0041
| | - Hongjun Zhang
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Boulevard, Tucson, AZ 85721-0041
| | - F. Ann Walker
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Boulevard, Tucson, AZ 85721-0041
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