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Analysis of institutional authors

Fernandez Pacios, LuisAuthorAlbareda, MartaAuthorPalacios, Jose-ManuelCorresponding AuthorImperial, JuanAuthor

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June 9, 2019
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Computational Study of the Fe(CN)(2)CO Cofactor and Its Binding to HypC Protein

Publicated to: JOURNAL OF PHYSICAL CHEMISTRY B. 117 (43): 13523-13533 - 2013-10-31 117(43), DOI: 10.1021/jp407574n

Authors:

Albareda, M; Palacios, JM; Imperial, J; Pacios, LF
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Affiliations

Univ Politecn Madrid, CBGP, Madrid 28223, Spain - Author
UPM, CBGP, CSIC, Madrid 28223, Spain - Author
UPM, ETSI Agronomos, Dept Biotecnol, Madrid 28040, Spain - Author
UPM, ETSI Montes, Dept Biotecnol, Madrid 28040, Spain - Author
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Abstract

In the intricate maturation process of [NiFe]-hydrogenases, the Fe(CN)(2)CO cofactor is first assembled in a HypCD complex with iron coordinated by cysteines from both proteins and CO is added after ligation of cyanides. The small accessory protein HypC is known to play a role in delivering the cofactor needed for assembling the hydrogenase active site. However, the chemical nature of the Fe(CN)(2)CO moiety and the stability of the cofactor-HypC complex are open questions. In this work, we address geometries, properties, and the nature of bonding of all chemical species involved in formation and binding of the cofactor by means of quantum calculations. We also study the influence of environmental effects and binding to cysteines on vibrational frequencies of stretching modes of CO and CN used to detect the presence of Fe(CN)(2)CO. Carbon monoxide is found to be much more sensitive to sulfur binding and the polarity of the medium than cyanides. The stability of the HypC-cofactor complex is analyzed by means of molecular dynamics simulation of cofactor-free and cofactor-bound forms of HypC. The results show that HypC is stable enough to carry the cofactor, but since its binding cysteine is located at the N-terminal unstructured tail, it presents large motions in solution, which suggests the need for a guiding interaction to achieve delivery of the cofactor.
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Keywords

Active-siteBacterial proteinsBinding sitesCarbon monoxideChemical-shiftsCrystal-structuresCyanidesEscherichia-coliFerrous compoundsForce-fieldLarge subunitModels, molecularMolecular-dynamicsNife hydrogenaseQuantum theoryRhizobium leguminosarumRhizobium-leguminosarumSwiss-model

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal JOURNAL OF PHYSICAL CHEMISTRY B due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2013, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Surfaces, Coatings and Films. Notably, the journal is positioned above the 90th percentile.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-25:

  • WoS: 5
  • Scopus: 6
  • Europe PMC: 3
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-25:

  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 23 (PlumX).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://oa.upm.es/26420/

As a result of the publication of the work in the institutional repository, statistical usage data has been obtained that reflects its impact. In terms of dissemination, we can state that, as of

  • Views: 370
  • Downloads: 4
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Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (ALBAREDA CONTRERAS, MARTA) and Last Author (Pacios, Luis F.).

the authors responsible for correspondence tasks have been PALACIOS ALBERTI, JOSE MANUEL and Pacios, Luis F..

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Awards linked to the item

We deeply thank Prof. Jorge Seminario and Dr. Dahiyana Cristancho (Texas A&M University) for their help in kindly providing us the force constants set for Fe(CN)2CO cofactor obtained with an unreleased new version of their program FUERZA. We also thank Madrid Supercomputing and Visualization Center (CeSViMa) for providing supercomputer resources (Magerit cluster), technical expertise, and assistance under projects G52225 and G52234. The authors acknowledge financial support as follows: M.A. from Microambiente-CM project, J.-M.P. from the Spanish Ministry of Science, project BIO2010-15301, J.I. from Fundacion Ramon Areces, XV Concurso Nacional de Ayuda para la Investigacion en Ciencias de la Vida y de la Materia, and L.F.P. from the Spanish Ministry of Science, project BIO2009-07050.
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