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Mai M, Zazubovich V, Mansbach RA. Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations. J Phys Chem B 2024; 128:1371-1384. [PMID: 38299975 PMCID: PMC10876061 DOI: 10.1021/acs.jpcb.3c06889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Reversible light and thermally induced spectral shifts are universally observed in a wide variety of pigment-protein complexes at temperatures ranging from cryogenic to ambient. In this paper, we employed large-scale molecular dynamics (MD) simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. From simulations of the water-soluble chlorophyll-binding protein complex, we determined that rearrangements of long hydrogen bonds were unlikely to be the origin of the multiwell landscape features necessary to explain observed spectral shifts. We also assessed small motions of amino acid residues and identified side chain rotations of some of these residues as likely candidates for the origin of relevant multiwell landscape features. The protein free-energy landscapes associated with side chain rotations feature energy barriers of around 1100-1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric triple-well landscape and moment of inertia of a relevant magnitude.
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Affiliation(s)
- Martina Mai
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Valter Zazubovich
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Rachael A. Mansbach
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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2
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Kapp-Joswig JO, Keller BG. CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering. J Chem Inf Model 2023; 63:1093-1098. [PMID: 36744824 DOI: 10.1021/acs.jcim.2c01493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Density-based clustering procedures are widely used in a variety of data science applications. Their advantage lies in the capability to find arbitrarily shaped and sized clusters and robustness against outliers. In particular, they proved effective in the analysis of molecular dynamics simulations, where they serve to identify relevant, low-energetic molecular conformations. As such, they can provide a convenient basis for the construction of kinetic (core-set) Markov-state models. Here we present the open-source Python project CommonNNClustering, which provides an easy-to-use and efficient reimplementation of the common-nearest-neighbor (CommonNN) method. The package provides functionalities for hierarchical clustering and an evaluation of the results. We put our emphasis on a generic API design to keep the implementation flexible and open for customization.
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Affiliation(s)
- Jan-Oliver Kapp-Joswig
- Department of Theoretical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195Berlin, Germany
| | - Bettina G Keller
- Department of Theoretical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195Berlin, Germany
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3
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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4
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Bouargalne Y, Raguénès-Nicol C, Guilbaud F, Cheron A, Clouet V, Deleu C, Le Cahérec F. New insights into chlorophyll-WSCP (water-soluble chlorophyll proteins) interactions : The case study of BnD22 (Brassica napus drought-induced 22 kDa). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 181:71-80. [PMID: 35452956 DOI: 10.1016/j.plaphy.2022.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/01/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The water-soluble chlorophyll-proteins (WSCP) of class II from Brassicaceae are non-photosynthetic proteins that bind chlorophylls (Chls) and chlorophyll derivatives. Their physiological roles, biochemical functions and mode of action are still unclear. It is assumed that the WSCPs have a protection function against Chl photodamage during stressful conditions. WSCPs are subdivided into class IIA and class IIB according to their apparent Chla/b binding ratio. Although their Chla/Chlb binding selectivity has been partly characterized, their Chl affinities are not yet precisely defined. For instance, WSCPs IIA do not show any Chl binding preference while WSCPs IIB have greater affinity to Chlb. In this study, we present a novel method for assessment of Chl binding to WSCPs based on the differences of Chl photobleaching rates in a large range of Chl/protein ratios. The protein we have chosen to study WSCP is BnD22, a WSCP IIA induced in the leaves of Brassica napus under water deficit. BnD22 formed oligomeric complexes upon binding to Chla and/or Chlb allowing a protective effect against photodamage. The binding constants indicate that BnD22 binds with high affinity the Chls and with a strong selectivity to Chla. Moreover, dependending of Chl/protein ratio upon reconstitution, two distinct binding events were detected resulting from difference of Chl stoichiometry inside oligomeric complexes.
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Affiliation(s)
- Youssef Bouargalne
- Univ Rennes 1, INRAE, Institut Agro, IGEPP - UMR 1349, 35653, Le Rheu, France
| | | | - Florian Guilbaud
- Univ Rennes 1, INRAE, Institut Agro, IGEPP - UMR 1349, 35653, Le Rheu, France
| | | | - Vanessa Clouet
- Univ Rennes 1, INRAE, Institut Agro, IGEPP - UMR 1349, 35653, Le Rheu, France
| | - Carole Deleu
- Univ Rennes 1, INRAE, Institut Agro, IGEPP - UMR 1349, 35653, Le Rheu, France
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Petry S, Götze JP. Effect of protein matrix on CP29 spectra and energy transfer pathways. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148521. [PMID: 34896078 DOI: 10.1016/j.bbabio.2021.148521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/25/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
We investigate energy transfer pathways between strongly coupled chlorophylls (Chls) in the CP29 (LHCII B4.1) antenna complex of Pisum sativum, including the possibility of higher energy states. We test for the environmental effects caused by the protein, membrane and solvent using a hybrid QM/MM approach. Classical molecular dynamics simulations of the full CP29 complex embedded in a DOPC membrane have been performed, followed by calculations of the time dependent DFT spectra of all Chls at several timesteps. The relative orientations of transition dipole moments (TDMs) were specifically analyzed, including and excluding the point charge field (PCF) of the surrounding environment. The PCF is found to drastically shift the spectra of specific Chls, while the majority of Chls is mostly unaffected. The net effect on the sum spectrum is however found to be negligible: The few strong changes in Chl spectra cancel each other due to being opposite in sign. We further find that the spectra of the Chls coordinating to water show a blue shift upon introduction of the environment. Conversely, the spectra of the Chls coordinating to glutamine show a red shift upon activation of the PCF. As the main influence of the PCF for tuning the couplings, we identify the energetic position of the individual chromophores. The fine-tuning, especially for states energetically above the Qy state, is however controlled by the changes in the TDM orientations. We also find an indication for the PCF to steer potentially harmful high energy excitations away from the PSII core complex.
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Affiliation(s)
- S Petry
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - J P Götze
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
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