1
|
Hu J, Park SJ, Walter T, Orozco IJ, O'Dea G, Ye X, Du J, Lü W. Physiological temperature drives TRPM4 ligand recognition and gating. Nature 2024; 630:509-515. [PMID: 38750366 PMCID: PMC11168932 DOI: 10.1038/s41586-024-07436-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/17/2024] [Indexed: 06/14/2024]
Abstract
Temperature profoundly affects macromolecular function, particularly in proteins with temperature sensitivity1,2. However, its impact is often overlooked in biophysical studies that are typically performed at non-physiological temperatures, potentially leading to inaccurate mechanistic and pharmacological insights. Here we demonstrate temperature-dependent changes in the structure and function of TRPM4, a temperature-sensitive Ca2+-activated ion channel3-7. By studying TRPM4 prepared at physiological temperature using single-particle cryo-electron microscopy, we identified a 'warm' conformation that is distinct from those observed at lower temperatures. This conformation is driven by a temperature-dependent Ca2+-binding site in the intracellular domain, and is essential for TRPM4 function in physiological contexts. We demonstrated that ligands, exemplified by decavanadate (a positive modulator)8 and ATP (an inhibitor)9, bind to different locations of TRPM4 at physiological temperatures than at lower temperatures10,11, and that these sites have bona fide functional relevance. We elucidated the TRPM4 gating mechanism by capturing structural snapshots of its different functional states at physiological temperatures, revealing the channel opening that is not observed at lower temperatures. Our study provides an example of temperature-dependent ligand recognition and modulation of an ion channel, underscoring the importance of studying macromolecules at physiological temperatures. It also provides a potential molecular framework for deciphering how thermosensitive TRPM channels perceive temperature changes.
Collapse
Affiliation(s)
- Jinhong Hu
- Van Andel Institute, Grand Rapids, MI, USA
| | | | - Tyler Walter
- Van Andel Institute, Grand Rapids, MI, USA
- Zoetis, Kalamazoo, MI, USA
| | - Ian J Orozco
- Van Andel Institute, Grand Rapids, MI, USA
- AnaBios, San Diego, CA, USA
| | | | - Xinyu Ye
- Van Andel Institute, Grand Rapids, MI, USA
| | - Juan Du
- Van Andel Institute, Grand Rapids, MI, USA.
| | - Wei Lü
- Van Andel Institute, Grand Rapids, MI, USA.
| |
Collapse
|
2
|
Dong XY, Liu R, Seroski DT, Hudalla GA, Hall CK. Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations. PLoS Comput Biol 2023; 19:e1011685. [PMID: 38048311 PMCID: PMC10729967 DOI: 10.1371/journal.pcbi.1011685] [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: 06/13/2023] [Revised: 12/19/2023] [Accepted: 11/13/2023] [Indexed: 12/06/2023] Open
Abstract
Co-assembling peptides can be crafted into supramolecular biomaterials for use in biotechnological applications, such as cell culture scaffolds, drug delivery, biosensors, and tissue engineering. Peptide co-assembly refers to the spontaneous organization of two different peptides into a supramolecular architecture. Here we use molecular dynamics simulations to quantify the effect of anionic amino acid type on co-assembly dynamics and nanofiber structure in binary CATCH(+/-) peptide systems. CATCH peptide sequences follow a general pattern: CQCFCFCFCQC, where all C's are either a positively charged or a negatively charged amino acid. Specifically, we investigate the effect of substituting aspartic acid residues for the glutamic acid residues in the established CATCH(6E-) molecule, while keeping CATCH(6K+) unchanged. Our results show that structures consisting of CATCH(6K+) and CATCH(6D-) form flatter β-sheets, have stronger interactions between charged residues on opposing β-sheet faces, and have slower co-assembly kinetics than structures consisting of CATCH(6K+) and CATCH(6E-). Knowledge of the effect of sidechain type on assembly dynamics and fibrillar structure can help guide the development of advanced biomaterials and grant insight into sequence-to-structure relationships.
Collapse
Affiliation(s)
- Xin Y. Dong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Renjie Liu
- Department of Biomedical Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Dillon T. Seroski
- Department of Biomedical Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Gregory A. Hudalla
- Department of Biomedical Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| |
Collapse
|
3
|
Zhang H, Dou Z, Bi W, Yang C, Wu X, Wang L. Multi-omics study of sulfur metabolism affecting functional microbial community succession during aerobic solid-state fermentation. BIORESOURCE TECHNOLOGY 2023; 387:129664. [PMID: 37573975 DOI: 10.1016/j.biortech.2023.129664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Microbial-mediated sulfur metabolism is closely related to carbon and nitrogen metabolism in natural biological systems. In this study, the effects of sulfur metabolism on microbial communities and functional enzyme succession were investigated based on integrated multi-omics by adding sulfur-containing compounds to aerobic fermentation systems. Sulfur powder was oxidized to S2O32- and subsequently to SO42- by the microbial sulfur-oxidizing system, which lowered the pH to 7.5 on day 7. The decrease in pH resulted in Planifilum (secreted S8, M17 and M32 proteases) losing its competitive advantage, whereas Novibacillus (secreted M14 and M19 metalloproteases) became dominant. Structural proteomics indicated that the surface of Novibacillus proteases has more negatively charged amino acid residues that help maintain protein stability at low pH. These findings aid understanding of the effects of sulfur metabolism on fermentation and the mechanism of microbial adaptation after pH reduction, providing new perspectives on the optimization of fermentation processes.
Collapse
Affiliation(s)
- Hong Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Zhixin Dou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wenhui Bi
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Faculty of Food Science and Engineering, Shandong Agricultural and Engineering University, Jinan, Shandong 250100, China
| | - Chuanlun Yang
- Shandong Chambroad Holding Group Co., Ltd., Boxing 256599, China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| |
Collapse
|
4
|
Liu Y, Zhang Q, Du J, Guo R. Arginine-rich peptides as crystallization inhibitors for sodium urate. J Mater Chem B 2023; 11:7389-7400. [PMID: 37431691 DOI: 10.1039/d3tb00666b] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Inhibiting the formation of urate crystals is the key to prevent hyperuricemia from developing into gout. Although many studies have focused on the influence of biomacromolecules in the crystallization behavior of sodium urate, the role of peptides with specific structures may contribute to unprecedented regulatory effects. Here, for the first time, we studied the effects of cationic peptides on the phase behavior, crystallization kinetics, and size/morphology of urate crystals. The addition of protamine (PRTM, a typical natural arginine-rich peptide) prolongs the nucleation induction time of sodium urate and inhibits crystal nucleation effectively. PRTM binds to the surface of amorphous sodium urate (ASU) through the hydrogen bond and electrostatic attraction between guanidine groups and urate anions, which is conducive to maintaining the state of ASU and inhibiting crystal nucleation. Moreover, PRTM preferentially binds to the MSUM plane and leads to a significant reduction in the aspect ratio of MSUM filamentous crystals. Further studies showed that there are significant differences in the inhibiting effects of arginine-rich peptides with different chain lengths on the crystallization behavior of sodium urate. Both guanidine functional groups and peptide chain length determine the crystallization inhibiting effect of peptides simultaneously. The present work highlights the potential role of arginine peptides in inhibiting the crystallization of urate and provides new insights into the inhibition mechanism in the pathological biomineralization of sodium urate, demonstrating the possibility of using cationic peptides to treat gout.
Collapse
Affiliation(s)
- Yan Liu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, P. R. China.
| | - QianYa Zhang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, P. R. China.
| | - JiaMei Du
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, P. R. China.
| | - Rong Guo
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, P. R. China.
| |
Collapse
|
5
|
K C B, Nii T, Mori T, Katayama Y. Dynamic frustrated charge hotspots created by charge density modulation sequester globular proteins into complex coacervates. Chem Sci 2023; 14:6608-6620. [PMID: 37350836 PMCID: PMC10283495 DOI: 10.1039/d3sc00993a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023] Open
Abstract
This study presents a simple strategy for the sequestration of globular proteins as clients into synthetic polypeptide-based complex coacervates as a scaffold, thereby recapitulating the scaffold-client interaction found in biological condensates. Considering the low net charges of scaffold proteins participating in biological condensates, the linear charge density (σ) on the polyanion, polyethylene glycol-b-poly(aspartic acids), was reduced by introducing hydroxypropyl or butyl moieties as a charge-neutral pendant group. Complex coacervate prepared from the series of reduced-σ polyanions and the polycation, homo-poly-l-lysine, could act as a scaffold that sequestered various globular proteins with high encapsulation efficiency (>80%), which sometimes involved further agglomerations in the coacervates. The sequestration of proteins was basically driven by electrostatic interaction, and therefore depended on the ionic strength and charges of the proteins. However, based on the results of polymer partitioning in the coacervate in the presence or absence of proteins, charge ratios between cationic and anionic polymers were maintained at the charge ratio of unity. Therefore, the origin of the electrostatic interaction with proteins is considered to be dynamic frustrated charges in the complex coacervates created by non-neutralized charges on polymer chains. Furthermore, fluorescence recovery after photobleaching (FRAP) measurements showed that the interaction of side-chains and proteins changed the dynamic property of coacervates. It also suggested that the physical properties of the condensate are tunable before and after the sequestration of globular proteins. The present rational design approach of the scaffold-client interaction is helpful for basic life-science research and the applied frontier of artificial organelles.
Collapse
Affiliation(s)
- Biplab K C
- Graduate School of Systems Life Sciences, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Teruki Nii
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Molecular Systems, Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Advanced Medical Open Innovation, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
- Department of Biomedical Engineering, Chung Yuan Christian University 200 Chung Pei Rd. Chung Li Taiwan 32023 ROC
| |
Collapse
|
6
|
Li N, Huang X, Shao H. Exploring the pH Sensitivity of Ion-Pair Interactions on a Self-Assembled Monolayer by Scanning Electrochemical Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:6529-6538. [PMID: 37116313 DOI: 10.1021/acs.langmuir.3c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Insights into the chemical essence of weak interactions on the surface of biomacromolecules may help to regulate biological processes. In this work, the pH sensitivity of ion-pair interactions occurring on a cysteine self-assembled monolayer (Cys SAM) that simulates the local surface of a protein was probed by scanning electrochemical microscopy (SECM). Cys SAM and the ion-pair interactions subsequently formed with the introduced aspartic acid (Asp) were both pH-sensitive, as confirmed by the tip current changes in the feedback mode. After continuous pH measurements, the most significant negative feedback was observed at pH 5.50, indicating the most robust ion-pair interactions, which were simultaneously identified by voltammetry. In this case, the extra addition of the inorganic cation (i.e., Ca2+) did not disrupt the existing ion-pair interactions, and the binding constant (K) and Gibbs free energy (ΔGo) of the ion pair were finally determined to be 6.44 × 105 M-1 and -33.14 kJ mol-1, respectively. Overall, the pH sensitivity of ion-pair interactions was found to be mainly attributable to pH-induced changes in the deprotonated/protonated states of the α-amino acid moieties, which may provide insights into the artificial manipulation of complex binding events at the molecular level on the biological surface.
Collapse
Affiliation(s)
- Na Li
- Key Laboratory of Cluster Science (Ministry of Education), Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing102488, P. R. China
| | - Ximing Huang
- School of Food and Chemical Engineering, Shaoyang University, Shaoyang 422000, Hunan, P. R. China
| | - Huibo Shao
- Key Laboratory of Cluster Science (Ministry of Education), Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing102488, P. R. China
| |
Collapse
|
7
|
Sauve S, Williamson J, Polasa A, Moradi M. Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters. MEMBRANES 2023; 13:membranes13050462. [PMID: 37233523 DOI: 10.3390/membranes13050462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences of the conformational dynamics of three different classes of transporters.
Collapse
Affiliation(s)
- Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Joseph Williamson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| |
Collapse
|
8
|
Li S, Mori M, Yang M, Elfazazi S, Hortigüela R, Chan P, Feng X, Risinger A, Yang Z, Oliva MÁ, Fernando Díaz J, Fang WS. Targeting the tubulin C-terminal tail by charged small molecules. Org Biomol Chem 2022; 21:153-162. [PMID: 36472095 DOI: 10.1039/d2ob01910h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The disordered tubulin C-terminal tail (CTT), which possesses a higher degree of heterogeneity, is the target for the interaction of many proteins and cellular components. Compared to the seven well-described binding sites of microtubule-targeting agents (MTAs) that localize on the globular tubulin core, tubulin CTT is far less explored. Therefore, tubulin CTT can be regarded as a novel site for the development of MTAs with distinct biochemical and cell biological properties. Here, we designed and synthesized linear and cyclic peptides containing multiple arginines (RRR), which are complementary to multiple acidic residues in tubulin CTT. Some of them showed moderate induction and promotion of tubulin polymerization. The most potent macrocyclic compound 1f was found to bind to tubulin CTT and thus exert its bioactivity. Such RRR containing compounds represent a starting point for the discovery of tubulin CTT-targeting agents with therapeutic potential.
Collapse
Affiliation(s)
- Shuo Li
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines & MHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nan Wei Road, Beijing 100050, China.
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Mingyan Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines & MHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nan Wei Road, Beijing 100050, China.
| | - Soumia Elfazazi
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Rafael Hortigüela
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Peter Chan
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Xinyue Feng
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang 524088, China
| | - April Risinger
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Zhiyou Yang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang 524088, China
| | - María Ángela Oliva
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid 28040, Spain
| | - J Fernando Díaz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Wei-Shuo Fang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines & MHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nan Wei Road, Beijing 100050, China.
| |
Collapse
|
9
|
Kim S, Kim JM, Wood K, Choi SH. Ionic group-dependent structure of complex coacervate hydrogels formed by ABA triblock copolymers. SOFT MATTER 2022; 18:4146-4155. [PMID: 35583260 DOI: 10.1039/d2sm00255h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study investigates the nanostructure of complex coacervate core hydrogels (C3Gs) with varying compositions of cationic charged groups (i.e., ammonium and guanidinium) using small-angle X-ray/neutron scattering (SAX/NS). C3Gs were prepared by stoichiometric mixing of two oppositely charged ABA triblock copolymers in aqueous solvents, in which A end-blocks were functionalized with either sulfonate groups or a mixture of ammonium and guanidinium groups. Comprehensive small-angle X-ray/neutron scattering (SAX/NS) analysis elucidated the dependence of C3Gs structures on the fraction of guanidinium groups in the cationic end-block (x) and salt concentration (cs). As x increases, the polymer volume fraction in the cores, and interfacial tension (γcore) and salt resistance (c*) of the coacervate cores increase, which is attributed to the greater hydrophobicity and non-electrostatic association. Furthermore, we observed that the salt dependence of the interfacial tension follows γcore ∼ (1 - cs/c*)3/2 in all series of x. The results show that the variation of the ionic group provides a powerful method to control the salt-responsiveness of C3Gs as stimuli-responsive materials.
Collapse
Affiliation(s)
- Seyoung Kim
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
| | - Jung-Min Kim
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
| | - Kathleen Wood
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Soo-Hyung Choi
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
| |
Collapse
|
10
|
Tiwari MK, Murarka RK. Interaction strength of osmolytes with the anion of a salt-bridge determines its stability. Phys Chem Chem Phys 2021; 23:5527-5539. [PMID: 33651069 DOI: 10.1039/d0cp05378c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to understand the role of osmolytes in regulating physicochemical behavior of proteins, we investigated the influence of protein destabilizing (urea and guanidinium chloride) and stabilizing osmolytes (TMAO, glycerol, and betaine) on a model salt-bridge (SB) formed between structural analogues of arginine and glutamate/aspartate sidechains in a solvent continuum using first-principles quantum chemical calculations based on DFT and MP2 methods. The binding strength of the osmolyte with the SB is found to be in the order of betaine > TMAO > Gdm+ > glycerol > urea. The osmolytes (TMAO and betaine) that preferentially bind to the SB cation have a marginal influence on SB stability. Also, pure π-π stacking interaction between Gdm+ and the SB cation plays an insignificant role in destabilizing the SB. In fact, the interaction strength of osmolytes with the SB anion mainly determines the stability of SB. For instance, a competition between Gdm+ and the SB cation to bind with the SB anion is responsible for instability and subsequent dissociation of the SB. The competition provided by other osmolytes is too weak to break the SB. Exploiting this information, we designed three structural derivatives of Gdm+, all having a stronger interaction with SB anion, and thereby show a stronger SB dissociation potential. Furthermore, we find an excellent linear anti-correlation between SB interaction energy and the energy of interaction between osmolyte and the SB anion, which suggests that by knowing only the strength of osmolyteacetate interaction, one can predict the influence of osmolytes on the salt-bridge instability. This information is useful in fine-tuning the SB dissociation power of Gdm+, which has a practical significance in obtaining the mechanistic insight into the influence of GdmCl on protein stability. Our results also provide a basis for understanding the chemistry of other ion-pairs formed between a cationic hydrogen donor and an anionic acceptor.
Collapse
Affiliation(s)
- Mrityunjay K Tiwari
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
| | - Rajesh K Murarka
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
| |
Collapse
|
11
|
Bashir M, Yousuf I, Arjmand F, Tabassum S. Deciphering the effect of hydrophobicity on protein binding interaction in cobalt(II) complexes by multispectroscopic and computational methods. J Biomol Struct Dyn 2021; 40:7381-7393. [PMID: 33685362 DOI: 10.1080/07391102.2021.1897678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In the present work, we report the synthesis, characterization of two cobalt complexes (1 and 2) and their HSA binding studies by multispectroscopic methods. Hirshfeld surfaces analysis and fingerprint plot analysis were carried out to identify intermolecular interactions viz., N-H···O, O-H···O and C-H···O linkages in crystal framework of the complexes. Density functional theory (DFT) studies were carried out to ascertain the electronic structure and molecular geometry of the complexes 1 and 2, and determine the localization of HOMO and LUMO in the complexes. A comparative in vitro interaction study of complex 1 and 2 with human serum albumin protein was carried out by employing UV-vis, fluorescence, circular dichroism, FTIR and molecular docking techniques. Interestingly, the HSA binding affinity of complex 2 was found to be more than complex 1 which was evidenced from the higher binding constant values owing to its strong hydrophobic topology. Further, a significant conformational change in microenvironment of HSA was noticed upon binding with complexes 1 and 2, nevertheless more perturbations were noticed in presence of complex 1. Molecular docking studies were carried out to validate the spectroscopic results and ascertain the preferential binding mode of complexes at the specific target site of HSA.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Masrat Bashir
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Imtiyaz Yousuf
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| |
Collapse
|
12
|
Simoes-Cardoso JC, Kojo H, Yoshimoto N, Yamamoto S. Microcalorimetric Analysis of the Adsorption of Lysozyme and Cytochrome c onto Cation-Exchange Chromatography Resins: Influence of Temperature on Retention. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:3336-3345. [PMID: 32160753 DOI: 10.1021/acs.langmuir.0c00197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We studied the adsorption mechanism of two basic proteins, equine cytochrome c (Cyt) and chicken egg-white lysozyme (Lys), adsorbing onto negatively charged chromatography surfaces. In liquid chromatography, the retention volume of Lys was larger than that of Cyt on negatively charged ion-exchange resins. When the temperature increased, the retention volume of Cyt increased, whereas that of Lys clearly decreased. Both Lys and Cyt share similar physical characteristics, so the opposite behavior with increasing temperatures was surprising, indicating a more complex mechanism of adsorption may be involved. We analyzed the adsorption of these proteins by using isothermal titration calorimetry (ITC). The change in adsorption enthalpy determined by ITC allowed the understanding of the reason for and underlying driving forces of protein adsorption that resulted in this opposite behavior. Large exothermic enthalpies of adsorption were observed for Lys (-43.95 kJ/mol), and Lys adsorption was found to be enthalpically driven. On the other hand, endothermic enthalpies were dominant for Cyt adsorption (32.41 kJ/mol), which was entropically driven. These results indicate that dehydration and release of counterions play a more important role in Cyt adsorption and ionic interaction and hydrogen bridges are more significant in Lys adsorption. Understanding of the adsorption mechanism of proteins onto chromatography resins is essential for modeling and developing new, efficient chromatographic processes.
Collapse
Affiliation(s)
- Joao C Simoes-Cardoso
- Bio-Process Engineering Laboratory, Biomedical Engineering Center, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| | - Hiroshi Kojo
- Bio-Process Engineering Laboratory, Biomedical Engineering Center, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| | - Noriko Yoshimoto
- Bio-Process Engineering Laboratory, Biomedical Engineering Center, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| | - Shuichi Yamamoto
- Bio-Process Engineering Laboratory, Biomedical Engineering Center, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| |
Collapse
|
13
|
Miller S, Yamada Y, Patel N, Suárez E, Andrews C, Tau S, Luke BT, Cachau RE, Schneider JP. Electrostatically Driven Guanidinium Interaction Domains that Control Hydrogel-Mediated Protein Delivery In Vivo. ACS CENTRAL SCIENCE 2019; 5:1750-1759. [PMID: 31807676 PMCID: PMC6891851 DOI: 10.1021/acscentsci.9b00501] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 05/10/2023]
Abstract
Protein biologics are an important class of drugs, but the necessity for frequent parenteral administration is a major limitation. Drug-delivery materials offer a potential solution, but protein-material adsorption can cause denaturation, which reduces their effectiveness. Here, we describe a new protein delivery platform that limits direct contact between globular protein domains and material matrix, yet from a single subcutaneous administration can be tuned for long-term drug release. The strategy utilizes complementary electrostatic interactions made between a suite of designed interaction domains (IDs), installed onto the terminus of a protein of interest, and a negatively charged self-assembled fibrillar hydrogel. These intermolecular interactions can be easily modulated by choice of ID to control material interaction and desorption energies, which allows regulation of protein release kinetics to fit desired release profiles. Molecular dynamics studies provided a molecular-level understanding of the mechanisms that govern release and identified optimal binding zones on the gel fibrils that facilitate strong ID-material interactions, which are crucial for sustained release of protein. This delivery platform can be easily loaded with cargo, is shear-thin syringe implantable, provides improved protein stability, is capable of a diverse range of in vitro release rates, and most importantly, can accomplish long-term control over in vivo protein delivery.
Collapse
Affiliation(s)
- Stephen
E. Miller
- Chemical
Biology Laboratory and Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yuji Yamada
- Chemical
Biology Laboratory and Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Nimit Patel
- Small Animal Imaging Program and Advanced Biomedical Computational Science Group, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ernesto Suárez
- Small Animal Imaging Program and Advanced Biomedical Computational Science Group, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Caroline Andrews
- Chemical
Biology Laboratory and Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Steven Tau
- Chemical
Biology Laboratory and Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Brian T. Luke
- Small Animal Imaging Program and Advanced Biomedical Computational Science Group, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Raul E. Cachau
- Small Animal Imaging Program and Advanced Biomedical Computational Science Group, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Joel P. Schneider
- Chemical
Biology Laboratory and Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| |
Collapse
|
14
|
Skvarnavičius G, Dvareckas D, Matulis D, Petrauskas V. Thermodynamics of Interactions Between Charged Surfactants and Ionic Poly(amino acids) by Isothermal Titration Calorimetry. ACS OMEGA 2019; 4:17527-17535. [PMID: 31656925 PMCID: PMC6812127 DOI: 10.1021/acsomega.9b02425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/18/2019] [Indexed: 05/04/2023]
Abstract
Interactions between charges play a role in protein stability and contribute to the energetics of binding between various charged ligands. Ionic surfactants are charged molecules, whose interactions with proteins are still rather poorly understood despite their wide applications. Here, we show by isothermal titration calorimetry that cationic alkylammonium surfactants bind to negatively charged polyaspartate and polyglutamate homopolymers stoichiometrically, i.e., one surfactant molecule per charged amino acid. Similarly, negatively charged alkyl sulfates (e.g., sodium dodecyl sulfate) and alkane sulfonates bind stoichiometrically to positively charged polylysine, polyornithine, and polyarginine homopolymers. In these reactions, the interacting counterparts form ion pairs and the resulting electrostatically neutral complex coprecipitates from solution. The enthalpies and heat capacities are determined for various pairs of ionic surfactants and charged amino acid homopolymers. These results show the energetic contributions of ionic headgroups and the CH2 group to surfactant interactions with proteins.
Collapse
|
15
|
Mason PE, Jungwirth P, Duboué-Dijon E. Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics. J Phys Chem Lett 2019; 10:3254-3259. [PMID: 31125523 DOI: 10.1021/acs.jpclett.9b01309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The molecular structure and strength of a model salt bridge between a guanidinium cation (side chain group of arginine) and the acetate carboxylic group in an aqueous solution is characterized by a combination of neutron diffraction with isotopic substitution and molecular dynamics simulations. The present neutron scattering experiments provide direct information about ion pairing in the solution. At the same time, these measurements are used to assess the quality of the force field employed in the simulation. We show that a standard nonpolarizable force field overestimates the strength of salt bridges. In contrast, accounting for electronic polarization effects via charge scaling allows to quantitatively reproduce the experiment. Such simulations are used to quantify the weak character of a fully hydrated salt bridge. Finally, on top of the canonical hydrogen-bonding binding mode, we uncover another interaction motif involving an out-of-plane hydrophobic contact of the acetate methyl group with the guanidinium cation.
Collapse
Affiliation(s)
- Philip E Mason
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo, nam. 2 , 16610 Prague 6 , Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo, nam. 2 , 16610 Prague 6 , Czech Republic
| | - Elise Duboué-Dijon
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo, nam. 2 , 16610 Prague 6 , Czech Republic
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie , 75005 , Paris , France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris , France
| |
Collapse
|
16
|
Kudriaeva A, Kuzina ES, Zubenko O, Smirnov IV, Belogurov A. Charge‐mediated proteasome targeting. FASEB J 2019; 33:6852-6866. [DOI: 10.1096/fj.201802237r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Ekaterina S. Kuzina
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Oleg Zubenko
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
- Kazan Federal UniversityKazanRussian Federation
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
- Department of Fundamental MedicineLomonosov Moscow State UniversityMoscowRussian Federation
| |
Collapse
|
17
|
Ahmed HH, Aglan HA, Mabrouk M, Abd-Rabou AA, Beherei HH. Enhanced mesenchymal stem cell proliferation through complexation of selenium/titanium nanocomposites. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2019; 30:24. [PMID: 30747346 DOI: 10.1007/s10856-019-6224-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
The main target of this work was to explore the proliferative impact of selenium dioxide nanoparticles (SeO2) and selenium dioxide/titanium dioxide nanocomposites (Se/Ti (I), (II) and (III)) on mesenchymal stem cells (MSCs). For this purpose, SeO2 and Se/Ti (I), (II) and (III) were prepared by facile one step method and characterized by transmission electron microscopy (TEM), Zetasizer, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscope (SEM) along with energy-dispersive X-ray spectrometry (EDX) with reference to SeO2 nanoparticles. Also, MSCs were isolated from rat bone marrow (BM-MSCs) and adipose tissue (ADSCs), propagated and characterized by flow cytometry. Thereafter, the proliferative effect of the fabricated nanomaterials was investigated by MTT assay. The TEM and DLS results, revealed that the average particle size of the suggested nanomaterials was in nanoscale. XRD pattern showed well crystalline structure for SeO2 nanoparticles and Se/Ti (I), (II) and (III) nanocomposites; the decreasing of the crystalline phase was observed by increasing the wt% of TiO2. The designed nanomaterials showed proliferative effects on MSCs with the most prominent effect exerted by 2 µg/ml of Se/Ti (III) and 5 µg/ml of Se/Ti (II) for ADSCs and 20 µg/ml of Se/Ti (II) and 10 µg/ml of Se/Ti (III) for BM-MSCs. Therefore, these newly designed nanomaterials have a promising influence on MSCs proliferation and they are recommended to be utilized in the filed of tissue engineering.
Collapse
Affiliation(s)
- Hanaa H Ahmed
- Hormones Department, National Research Centre, Giza, Egypt.
- Stem Cells Lab, Center of Excellence for Advanced Sciences, National Research Centre, Giza, Egypt.
| | - Hadeer A Aglan
- Hormones Department, National Research Centre, Giza, Egypt
- Stem Cells Lab, Center of Excellence for Advanced Sciences, National Research Centre, Giza, Egypt
| | - Mostafa Mabrouk
- Refractories, Ceramics and Building Materials Department, National Research Centre, Giza, Egypt
| | - Ahmed A Abd-Rabou
- Hormones Department, National Research Centre, Giza, Egypt
- Stem Cells Lab, Center of Excellence for Advanced Sciences, National Research Centre, Giza, Egypt
| | - Hanan H Beherei
- Refractories, Ceramics and Building Materials Department, National Research Centre, Giza, Egypt
| |
Collapse
|
18
|
Pylaeva S, Brehm M, Sebastiani D. Salt Bridge in Aqueous Solution: Strong Structural Motifs but Weak Enthalpic Effect. Sci Rep 2018; 8:13626. [PMID: 30206276 PMCID: PMC6133928 DOI: 10.1038/s41598-018-31935-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/29/2018] [Indexed: 12/03/2022] Open
Abstract
Salt bridges are elementary motifs of protein secondary and tertiary structure and are commonly associated with structural driving force that increases stability. Often found on the interface to the solvent, they are highly susceptible to solvent–solute interactions, primarily with water but also with other cosolvents (especially ions). We have investigated the interplay of an Arginine–Aspartic acid salt bridge with simple salt ions in aqueous solution by means of molecular dynamics simulations. Besides structural and dynamical features at equilibrium, we have computed the mean force along the dissociation pathway of the salt bridge. We demonstrate that solvated ions influence the behavior of the salt bridge in a very specific and local way, namely the formation of tight ionic pairs Li+/Na+–Asp−. Moreover, our findings show that the enthalpic relevance of the salt bridge is minor, regardless of the presence of solvated ions.
Collapse
Affiliation(s)
- Svetlana Pylaeva
- Martin Luther University Halle-Wittenberg, Institute of Physical Chemistry, 06120, Halle, Saale, Germany
| | - Martin Brehm
- Martin Luther University Halle-Wittenberg, Institute of Physical Chemistry, 06120, Halle, Saale, Germany
| | - Daniel Sebastiani
- Martin Luther University Halle-Wittenberg, Institute of Physical Chemistry, 06120, Halle, Saale, Germany.
| |
Collapse
|
19
|
Noresson AL, Aurelius O, Öberg CT, Engström O, Sundin AP, Håkansson M, Stenström O, Akke M, Logan DT, Leffler H, Nilsson UJ. Designing interactions by control of protein-ligand complex conformation: tuning arginine-arene interaction geometry for enhanced electrostatic protein-ligand interactions. Chem Sci 2017; 9:1014-1021. [PMID: 29675148 PMCID: PMC5883865 DOI: 10.1039/c7sc04749e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/01/2017] [Indexed: 01/13/2023] Open
Abstract
3-Benzamido-2-O-sulfo-galactosides can be designed to control protein conformation into forming entropically favourable galectin-3-arginine salt bridges with ligand sulfates.
We investigated galectin-3 binding to 3-benzamido-2-O-sulfo-galactoside and -thiodigalactoside ligands using a combination of site-specific mutagenesis, X-ray crystallography, computational approaches, and binding thermodynamics measurements. The results reveal a conformational variability in a surface-exposed arginine (R144) side chain in response to different aromatic C3-substituents of bound galactoside-based ligands. Fluorinated C3-benzamido substituents induced a shift in the side-chain conformation of R144 to allow for an entropically favored electrostatic interaction between its guanidine group and the 2-O-sulfate of the ligand. By contrast, binding of ligands with non-fluorinated substituents did not trigger a conformational change of R144. Hence, a sulfate–arginine electrostatic interaction can be tuned by the choice of ligand C3-benzamido structures to favor specific interaction modes and geometries. These results have important general implications for ligand design, as the proper choice of arginine–aromatic interacting partners opens up for ligand-controlled protein conformation that in turn may be systematically exploited in ligand design.
Collapse
Affiliation(s)
- A-L Noresson
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - O Aurelius
- Section for Biochemistry and Structural Biology , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden
| | - C T Öberg
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - O Engström
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - A P Sundin
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - M Håkansson
- SARomics Biostructures AB , Medicon Village , SE-223 81 Lund , Sweden
| | - O Stenström
- Biophysical Chemistry , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden
| | - M Akke
- Biophysical Chemistry , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden
| | - D T Logan
- Section for Biochemistry and Structural Biology , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden.,SARomics Biostructures AB , Medicon Village , SE-223 81 Lund , Sweden
| | - H Leffler
- Department of Laboratory Medicine , Section MIG , Lund University , Sölvegatan 23, SE-223 62 , Lund , Sweden
| | - U J Nilsson
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| |
Collapse
|
20
|
Zhang N, Wang Y, An L, Song X, Huang Q, Liu Z, Yao L. Entropy Drives the Formation of Salt Bridges in the Protein GB3. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ning Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; University of Chinese Academy of Sciences; Songling Road 189 Qingdao 266061 China
| | - Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; University of Chinese Academy of Sciences; Songling Road 189 Qingdao 266061 China
| | - Liaoyuan An
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; University of Chinese Academy of Sciences; Songling Road 189 Qingdao 266061 China
| | - Xiangfei Song
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; University of Chinese Academy of Sciences; Songling Road 189 Qingdao 266061 China
| | - Qingshan Huang
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; University of Chinese Academy of Sciences; Songling Road 189 Qingdao 266061 China
| | - Zhijun Liu
- Department National Center for Protein Science Shanghai; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Haike Road 333 Shanghai 201210 China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; University of Chinese Academy of Sciences; Songling Road 189 Qingdao 266061 China
| |
Collapse
|
21
|
Entropy Drives the Formation of Salt Bridges in the Protein GB3. Angew Chem Int Ed Engl 2017; 56:7601-7604. [DOI: 10.1002/anie.201702968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Indexed: 12/28/2022]
|
22
|
Hong T, Iwashita K, Handa A, Shiraki K. Arginine prevents thermal aggregation of hen egg white proteins. Food Res Int 2017; 97:272-279. [PMID: 28578052 DOI: 10.1016/j.foodres.2017.04.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/24/2017] [Accepted: 04/14/2017] [Indexed: 12/18/2022]
Abstract
The control of aggregation and solubilization of hen egg white protein (HEWP) is an important issue for industrial applications of one of the most familiar food protein sources. Here, we investigated the effects of edible amino acids on heat-induced aggregation of HEWP. The addition of 0.6M arginine (Arg) completely suppressed the formation of insoluble aggregates of 1mgmL-1 HEWP following heat treatment, even at 90°C for 20min. In contrast, lysine (Lys), glycine (Gly), and sodium chloride (NaCl) did little to suppress the aggregation of HEWP under the same conditions. SDS-PAGE indicated that Arg suppresses the thermal aggregation of almost all types of HEWP at 1mgmL-1. However, Arg did not suppress the thermal aggregation of HEWP at concentrations ≥10mgmL-1 and prompted the formation of aggregates. Transmission electron micrographs revealed a high-density structure of unfolded proteins in the presence of Arg. These results indicate that Arg exerts a greater suppressive effect on a protein mixture, such as HEWP, than on a single model protein. These observations may propose Arg as a safe and reasonable additive to HEWP for the elimination of microorganisms by allowing an increase in sterilization temperature.
Collapse
Affiliation(s)
- Taehun Hong
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kazuki Iwashita
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Akihiro Handa
- R&D Division, Kewpie Corporation, 2-5-7 Sengawa, Chofu, Tokyo 182-0002, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
| |
Collapse
|
23
|
Salehi A, Larson RG. A Molecular Thermodynamic Model of Complexation in Mixtures of Oppositely Charged Polyelectrolytes with Explicit Account of Charge Association/Dissociation. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01464] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ali Salehi
- Department of Chemical
Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ronald G. Larson
- Department of Chemical
Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
24
|
Kashcooli Y, Park K, Bose A, Greenfield M, Bothun GD. Patchy Layersomes Formed by Layer-by-Layer Coating of Liposomes with Strong Biopolyelectrolytes. Biomacromolecules 2016; 17:3838-3844. [DOI: 10.1021/acs.biomac.6b01467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yaser Kashcooli
- Department
of Chemical Engineering, University of Rhode Island, 16 Greenhouse
Road, Kingston, Rhode Island 02881, United States
| | - Keunhan Park
- Department
of Mechanical Engineering, University of Utah, 1495 E 100 S, Salt Lake City, Utah 84112, United States
| | - Arijit Bose
- Department
of Chemical Engineering, University of Rhode Island, 16 Greenhouse
Road, Kingston, Rhode Island 02881, United States
| | - Michael Greenfield
- Department
of Chemical Engineering, University of Rhode Island, 16 Greenhouse
Road, Kingston, Rhode Island 02881, United States
| | - Geoffrey D. Bothun
- Department
of Chemical Engineering, University of Rhode Island, 16 Greenhouse
Road, Kingston, Rhode Island 02881, United States
| |
Collapse
|
25
|
Lu D, Zhang Y, Li Y, Luo C, Wang X, Guan X, Ma H, Zhao X, Wei Q, Lei Z. Preparation and properties of reversible hydrogels based on triblock poly(amino acid)s with tunable pH-responsivity across a broad range. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/pola.28375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Dedai Lu
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Yongyong Zhang
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Yunfei Li
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Chen Luo
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Xiangya Wang
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Xiaolin Guan
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Hengchang Ma
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Xiaolong Zhao
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Qiangbing Wei
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| | - Ziqiang Lei
- Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education, Key Laboratory of Polymer Materials of Gansu Province, School of Chemistry and Chemical Engineering; Northwest Normal University; Lanzhou 730070 People's Republic of China
| |
Collapse
|
26
|
Qu X, Persson KA. Toward Accurate Modeling of the Effect of Ion-Pair Formation on Solute Redox Potential. J Chem Theory Comput 2016; 12:4501-8. [DOI: 10.1021/acs.jctc.6b00289] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaohui Qu
- Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kristin A. Persson
- Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
27
|
De Luca I, Di Salle A, Alessio N, Margarucci S, Simeone M, Galderisi U, Calarco A, Peluso G. Positively charged polymers modulate the fate of human mesenchymal stromal cells via ephrinB2/EphB4 signaling. Stem Cell Res 2016; 17:248-255. [PMID: 27591481 DOI: 10.1016/j.scr.2016.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/01/2016] [Accepted: 07/18/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding the mechanisms by which mesenchymal stromal cells (MSCs) interact with the physical properties (e.g. topography, charge, ζ-potential, and contact angle) of polymeric surfaces is essential to design new biomaterials capable of regulating stem cell behavior. The present study investigated the ability of two polymers (pHM1 and pHM3) with different positive surface charge densities to modulate the differentiation of MSCs into osteoblast-like phenotype via cell-cell ephrinB2/EphB4 signaling. Although pHM1 promoted the phosphorylation of EphB4, leading to cell differentiation, pHM3, characterized by a high positive surface charge density, had no significant effect on EphB4 activation or MSCs differentiation. When the MSCs were cultured on pHM1 in the presence of a forward signaling blocking peptide, the osteoblast differentiation was compromised. Our results demonstrated that the ephrinB2/EphB4 interaction was required for MSCs differentiation into an osteoblast-like phenotype and that the presence of a high positive surface charge density altered this interaction.
Collapse
Affiliation(s)
- Ilenia De Luca
- Institute of Bioscience and BioResources - CNR -, Naples, Italy
| | - Anna Di Salle
- Institute of Bioscience and BioResources - CNR -, Naples, Italy
| | - Nicola Alessio
- Department of Experimental Medicine, Biotechnology and Molecular Biology Section, Second University of Naples, Naples, Italy
| | | | - Michele Simeone
- Medical School "Federico II" Naples, Department of Neurosciences, Reproductive and Odontostomatologic Sciences, Naples, Italy
| | - Umberto Galderisi
- Department of Experimental Medicine, Biotechnology and Molecular Biology Section, Second University of Naples, Naples, Italy
| | - Anna Calarco
- Institute of Bioscience and BioResources - CNR -, Naples, Italy.
| | | |
Collapse
|
28
|
Altan I, Charbonneau P, Snell EH. Computational crystallization. Arch Biochem Biophys 2016; 602:12-20. [PMID: 26792536 DOI: 10.1016/j.abb.2016.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 12/22/2015] [Accepted: 01/07/2016] [Indexed: 11/28/2022]
Abstract
Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.
Collapse
Affiliation(s)
- Irem Altan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, NC 27708, USA; Department of Physics, Duke University, Durham, NC 27708, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St., NY 14203, USA; Department of Structural Biology, SUNY University of Buffalo, 700 Ellicott St., NY 14203, USA.
| |
Collapse
|