51
|
Sanchez OF, Mendonca A, Carneiro AD, Yuan C. Engineering Recombinant Protein Sensors for Quantifying Histone Acetylation. ACS Sens 2017; 2:426-435. [PMID: 28723212 DOI: 10.1021/acssensors.7b00026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
H3K14ac (acetylation of lysine 14 of histone H3) is one of the most important epigentic modifications. Aberrant changes in H3K14ac have been associated with various diseases, including cancers and neurological disorders. Tools that enable detection and quantification of H3K14ac levels in cell extracts and in situ are thus of critical importance to reveal its role in various biological processes. Current detection techniques of specific histone modifications, however, are constrained by tedious sample pretreatments, lack of quantitative accuracy, and reliance on high quality antibodies. To address this issue, we engineered recombinant sensors that are suitable for probing histone acetylation levels using various biological samples. The protein sensor contains recongition domain(s) with sequences derived from the bromodomain of human polybromo-1 (PB1), a natural H3K14ac reader domain. Various sensor designs were tested using nuclear extracts and live cells. The sensor containing dimeric repeats of bromodomain was found most effective in quantifying H3K14ac level in both in vitro and in situ assays. The sensor has a linear detection range of 0.5-50 nM when mixed with nuclear extracts. The sensor colocalizes with H3K14ac antibodies in situ when transfected into human embryonic kidney 293T (HEK293T) cells and is thus capable of providing spatial details of histone modification within the nucleus. Corrected nuclear fluorescence intensity was used to quantify the modification level in situ and found to correlate well with our in vitro assays. Our sensor offers a novel tool to characterize the histone modification level using nuclear extracts and probe histone modification change in live cells.
Collapse
Affiliation(s)
- Oscar F. Sanchez
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Agnes Mendonca
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Ana D. Carneiro
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Chongli Yuan
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| |
Collapse
|
52
|
Vasantha B, George G, Raghothama S, Balaram P. Homooligomeric β 3 (R)-valine peptides: Transformation between C 14 and C 12 helical structures induced by a guest Aib residue. Biopolymers 2017; 108. [PMID: 27539268 DOI: 10.1002/bip.22935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/08/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022]
Abstract
Novel helical, structures unprecedented in the chemistry of α-polypeptides, may be found in polypeptides containing β and γ amino acids. The structural characterization of C12 and C14 -helices in oligo β-peptides was originally achieved using conformationally constrained cyclic β-residues. This study explores the conformational characteristics of proteinogenic β3 residues in homooligomeric sequences and addresses the issue of inducing a transition between C14 and C12 helices by the introduction of a guest α-residue. Folded C14 -helical structures are demonstrated for the nonapeptide Boc-[β3 (R)Val]9 -OMe by NMR methods in CDCl3 -DMSO mixtures, while the peptide was found to be aggregated in CDCl3 . The insertion of a guest Aib residue into an oligo-β-valine sequence in the octapeptide model Boc-[(β3 (R)Val)3 -Aib-(β3 (R)Val]4 -OMe results in well dispersed NH region in the NMR spectrum indicating folded structures in CDCl3 . Structure calculations for both the peptides using NOE distance constraints support a C14 helical structure in the homooligomer which transform into a C12 helix on introduction of the guest Aib residue.
Collapse
Affiliation(s)
| | - Gijo George
- Department of Physics, NMR Research Center, Indian Institute of Science, Bangalore, 560012, India
| | | | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
| |
Collapse
|
53
|
Lin CW, Gai F. Microscopic nucleation and propagation rates of an alanine-based α-helix. Phys Chem Chem Phys 2017; 19:5028-5036. [PMID: 28165082 PMCID: PMC5359971 DOI: 10.1039/c6cp08924k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An infrared temperature-jump (T-jump) study by Huang et al. (Proc. Natl. Acad. Sci. U. S. A., 2002, 99, 2788-2793) showed that the conformational relaxation kinetics of an alanine-based α-helical peptide depend not only on the final temperature (Tf) but also on the initial temperature (Ti) when Tf is fixed. Their finding indicates that the folding free energy landscape of this peptide is non-two-state like, allowing for the population of conformational ensembles with different helical lengths and relaxation times in the temperature range of the experiment. Because α-helix folding involves two fundamental events, nucleation and propagation, the results of Huang et al. thus present a unique opportunity to determine their rate constants - a long-sought goal in the study of the helix-coil transition dynamics. Herein, we capitalize on this notion and develop a coarse-grained kinetic model to globally fit the thermal unfolding curve and T-jump kinetic traces of this peptide. Using this strategy, we are able to explicitly determine the microscopic rate constants of the kinetic steps encountered in the nucleation and propagation processes. Our results reveal that the time taken to form one α-helical turn (i.e., an α-helical segment with one helical hydrogen bond) is about 315 ns, whereas the time taken to elongate this nucleus by one residue (or backbone unit) is 5.9 ns, depending on the position of the residue.
Collapse
Affiliation(s)
- Chun-Wei Lin
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, USA.
| |
Collapse
|
54
|
Unraveling amyloid formation paths of Parkinson's disease protein α-synuclein triggered by anionic vesicles. Q Rev Biophys 2017; 50:e3. [DOI: 10.1017/s0033583517000026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractAmyloid formation of the synaptic brain proteinα-synuclein (αS) is related to degeneration of dopaminergic neurons in Parkinson's disease patients.αS is thought to function in vesicle transport and fusion and it binds strongly to negatively charged vesiclesin vitro. Here we combined circular dichroism, fluorescence and imaging methodsin vitroto characterize the interaction ofαS with negatively charged vesicles of DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, sodium salt) and DOPG (1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol), sodium salt) and the consequences of such interactions onαS amyloid formation. We found that lipid head-group chemistry modulatesαS interactions and also affects amyloid fiber formation. During the course of the experiments, we made the unexpected discovery that pre-formedαS oligomers, typically present in a small amount in theαS starting material, acted as templates for linear growth of anomalous amyloid fibers in the presence of vesicles. At the same time, the remainingαS monomers were restricted from vesicle-mediated nucleation of amyloid fibers. Although not a dominant process in bulk experiments, this hiddenαS aggregation pathway may be of importancein vivo.
Collapse
|
55
|
Preparation of the Extracellular Domain of Recombinant Human Toll-like Receptor 6. Protein J 2017; 36:28-35. [PMID: 28161794 DOI: 10.1007/s10930-016-9692-8] [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: 10/20/2022]
Abstract
Toll-like receptors (TLRs) mediate immune responses upon recognition of a variety of ligands. To further elucidate the function of TLRs, it is important to identify novel ligands and their action mechanisms including polymer assembly. In this study, we propose an efficient method for preparation of the extracellular domain of human Toll-like receptor 6 (TLR6ED) in Escherichia coli using the bubbling cultivation method. Our preparation method improved the level of expression of TLR6ED into a soluble fraction as compared with typical cultivation using a rotary shaker. Circular dichroism (CD) experiments confirmed the structural formation of TLR6ED with secondary structure contents similar to leucine-rich repeat (LRR) modules. In addition, we also provided a procedure for preparing this recombinant protein using Sf9 insect cells, which ensures preservation of some key posttranslational modifications often lacking in bacteria-expressed proteins. These materials would be useful for analyzing novel molecules that bind directly to TLR6, complex formations with other regulators including TLR2 and TLR4, and the functional effects of N-linked glycosylation.
Collapse
|
56
|
Dexter AF, Fletcher N, Creasey RG, Filardo F, Boehm MW, Jack KS. Fabrication and characterization of hydrogels formed from designer coiled-coil fibril-forming peptides. RSC Adv 2017. [DOI: 10.1039/c7ra02811c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A peptide sequence was designed to form α-helical fibrils and hydrogels at physiological pH, utilising transient buffering by carbonic acid.
Collapse
Affiliation(s)
- A. F. Dexter
- The University of Queensland
- Australian Institute for Bioengineering and Biotechnology
- Australia
| | - N. L. Fletcher
- The University of Queensland
- Australian Institute for Bioengineering and Biotechnology
- Australia
| | - R. G. Creasey
- The University of Queensland
- School of Chemical Engineering
- Australia
| | - F. Filardo
- The University of Queensland
- Australian Institute for Bioengineering and Biotechnology
- Australia
| | - M. W. Boehm
- The University of Queensland
- School of Chemical Engineering
- Australia
| | - K. S. Jack
- The University of Queensland
- Centre for Microscopy and Microanalysis
- Australia
| |
Collapse
|
57
|
Choi JW, Hong ST, Kang DE, Paik KC, Han MS, Lim CS, Cho BR. Two-Photon Tracer for Human Epidermal Growth Factor Receptor-2: Detection of Breast Cancer in a Live Tissue. Anal Chem 2016; 88:9412-9418. [DOI: 10.1021/acs.analchem.6b00912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ji-Woo Choi
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, 145
Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Seung Taek Hong
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, 145
Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Dong Eun Kang
- Department
of Chemistry, Korea University, 145 Anam-ro, Sungbuk-gu, Seoul, 02841, Republic of Korea
| | - Kyu Cheol Paik
- Department
of Chemistry, Daejin University, 1007 Hoguk-ro, Pochun-si, Gyeonggi-do 11159, Republic of Korea
| | - Man So Han
- Department
of Chemistry, Daejin University, 1007 Hoguk-ro, Pochun-si, Gyeonggi-do 11159, Republic of Korea
| | - Chang Su Lim
- Department
of Chemistry, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16499, Republic of Korea
| | - Bong Rae Cho
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, 145
Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Sungbuk-gu, Seoul, 02841, Republic of Korea
- Department
of Chemistry, Daejin University, 1007 Hoguk-ro, Pochun-si, Gyeonggi-do 11159, Republic of Korea
| |
Collapse
|
58
|
Brisbois CA, Lee JC. Apolipoprotein C-III Nanodiscs Studied by Site-Specific Tryptophan Fluorescence. Biochemistry 2016; 55:4939-48. [PMID: 27529357 DOI: 10.1021/acs.biochem.6b00599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Apolipoprotein C-III (ApoC-III) is found on high-density lipoproteins (HDLs) and remodels 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles into HDL-like particles known as nanodiscs. Using single-Trp-containing ApoC-III mutants, we have studied local side chain environments and interactions in nanodiscs at positions W42, W54, and W65. Using transmission electron microscopy and circular dichroism spectroscopy, nanodiscs were characterized at the ultrastructural and secondary conformational levels, respectively. Nearly identical particles (15 ± 2 nm) were produced from all proteins containing approximately 25 ± 4 proteins per particle with an average helicity of 45-51% per protein. Distinct residue-specific fluorescence properties were observed with W54 residing in the most hydrophobic environment followed by W42 and W65. Interestingly, time-resolved anisotropy measurements revealed that Trp side chain mobility is uncorrelated to the polarity of its surroundings. W54 is the most mobile compared to W65 and W42, which are more immobile in a nanodisc-bound state. On the basis of Trp spectral comparisons of ApoC-III in micellar and vesicle environments, ApoC-III binding within nanodiscs more closely resembles a bilayer-bound state. Despite the nanodiscs being structurally similar, we found marked differences during nanodisc formation by the Trp variants as a function of temperature, with W42 behaving the most like the wild-type protein. Our data suggest that despite the modest mutations of Trp to Phe at two of the three native sites, the interfacial location of W42 is important for lipid binding and nanodisc assembly, which may be biologically meaningful as of the three Trp residues, only W42 is invariant among mammals.
Collapse
Affiliation(s)
- Chase A Brisbois
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| |
Collapse
|
59
|
Calero-Rubio C, Paik B, Jia X, Kiick KL, Roberts CJ. Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation. Biophys Chem 2016; 217:8-19. [PMID: 27486699 DOI: 10.1016/j.bpc.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/14/2016] [Accepted: 07/17/2016] [Indexed: 10/21/2022]
Abstract
This report focuses on the molecular-level processes and thermodynamics of unfolding of a series of helical peptides using a coarse-grained (CG) molecular model. The CG model was refined to capture thermodynamics and structural changes as a function of temperature for a set of published peptide sequences. Circular dichroism spectroscopy (CD) was used to experimentally monitor the temperature-dependent conformational changes and stability of published peptides and new sequences introduced here. The model predictions were quantitatively or semi-quantitatively accurate in all cases. The simulations and CD results showed that, as expected, in most cases the unfolding of helical peptides is well described by a simply 2-state model, and conformational stability increased with increased length of the helices. A notable exception in a 19-residue helix was when two Ala residues were each replaced with Phe. This stabilized a partly unfolded intermediate state via hydrophobic contacts, and also promoted aggregates at higher peptide concentrations.
Collapse
Affiliation(s)
- Cesar Calero-Rubio
- Chemical & Biomolecular Engineering Department, University of Delaware, Newark, DE 19716, United States
| | - Bradford Paik
- Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States
| | - Xinqiao Jia
- Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States
| | - Kristi L Kiick
- Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States.
| | - Christopher J Roberts
- Chemical & Biomolecular Engineering Department, University of Delaware, Newark, DE 19716, United States.
| |
Collapse
|
60
|
Olivares-Quiroz L. Role of single-point mutations and deletions on transition temperatures in ideal proteinogenic heteropolymer chains in the gas phase. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2016; 45:393-403. [PMID: 26818963 DOI: 10.1007/s00249-015-1108-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/18/2015] [Accepted: 12/16/2015] [Indexed: 06/05/2023]
Abstract
A coarse-grained statistical mechanics-based model for ideal heteropolymer proteinogenic chains of non-interacting residues is presented in terms of the size K of the chain and the set of helical propensities [Formula: see text] associated with each residue j along the chain. For this model, we provide an algorithm to compute the degeneracy tensor [Formula: see text] associated with energy level [Formula: see text] where [Formula: see text] is the number of residues with a native contact in a given conformation. From these results, we calculate the equilibrium partition function [Formula: see text] and characteristic temperature [Formula: see text] at which a transition from a low to a high entropy states is observed. The formalism is applied to analyze the effect on characteristic temperatures [Formula: see text] of single-point mutations and deletions of specific amino acids [Formula: see text] along the chain. Two probe systems are considered. First, we address the case of a random heteropolymer of size K and given helical propensities [Formula: see text] on a conformational phase space. Second, we focus our attention to a particular set of neuropentapeptides, [Met-5] and [Leu-5] enkephalins whose thermodynamic stability is a key feature on their coupling to [Formula: see text] and [Formula: see text] receptors and the triggering of biochemical responses.
Collapse
Affiliation(s)
- L Olivares-Quiroz
- Colegio de Ciencia y Tecnologia and Posgrado en Ciencias de la Complejidad, Universidad Autonoma de la Ciudad de Mexico, Prol Av San Isidro 151, Deleg Iztapalapa, CP 09760, Mexico, DF, Mexico.
| |
Collapse
|
61
|
Thermal protein unfolding by differential scanning calorimetry and circular dichroism spectroscopy Two-state model versus sequential unfolding. Q Rev Biophys 2016; 49:e9. [PMID: 27658613 DOI: 10.1017/s0033583516000044] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Thermally-induced protein unfolding is commonly described with the two-state model. This model assumes only two types of protein molecules in solution, the native (N) and the denatured, unfolded (U) protein. In reality, protein unfolding is a multistep process, even if intermediate states are only sparsely populated. As an alternative approach we explore the Zimm-Bragg theory, originally developed for the α-helix-to-random coil transition of synthetic polypeptides. The theory includes intermediate structures with concentrations determined by the cooperativity of the unfolding reaction. We illustrate the differences between the two-state model and the Zimm-Bragg theory with measurements of apolipoprotein A-1 and lysozyme by differential scanning calorimetry (DSC) and CD spectroscopy. Nine further protein examples are taken from the literature. The Zimm-Bragg theory provides a perfect fit of the calorimetric unfolding transitions for all proteins investigated. In contrast, the transition curves and enthalpies predicted by the two-state model differ considerably from the experimental results. Apolipoprotein A-1 is ~50% α-helical at ambient temperature and its unfolding follows the classical α-helix-to-random coil equilibrium. The unfolding of proteins with little α-helix content, such as lysozyme, can also be analyzed with the Zimm-Bragg theory by introducing the concept of 'folded' and 'unfolded' peptide units assuming an average unfolding enthalpy per peptide unit. DSC is the method of choice to measure the unfolding enthalpy, , but CD spectroscopy in combination with the two-state model is often used to deduce the unfolding enthalpy. This can lead to erroneous result. Not only are different enthalpies required to describe the CD and DSC transition curves but these values deviate distinctly from the experimental result. In contrast, the Zimm-Bragg theory predicts the DSC and CD unfolding transitions with the same set of parameters.
Collapse
|
62
|
Takechi-Haraya Y, Nadai R, Kimura H, Nishitsuji K, Uchimura K, Sakai-Kato K, Kawakami K, Shigenaga A, Kawakami T, Otaka A, Hojo H, Sakashita N, Saito H. Enthalpy-driven interactions with sulfated glycosaminoglycans promote cell membrane penetration of arginine peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1339-49. [DOI: 10.1016/j.bbamem.2016.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/12/2016] [Accepted: 03/17/2016] [Indexed: 12/16/2022]
|
63
|
Dannenberg JJ. The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals. ACTA ACUST UNITED AC 2016; 72:227-73. [PMID: 16581379 DOI: 10.1016/s0065-3233(05)72009-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.
Collapse
Affiliation(s)
- J J Dannenberg
- Department of Chemistry, City University of New York, Hunter College and the Graduate School New York, New York 10021
| |
Collapse
|
64
|
Tian Y, Wang D, Li J, Shi C, Zhao H, Niu X, Li Z. A proline-derived transannular N-cap for nucleation of short α-helical peptides. Chem Commun (Camb) 2016; 52:9275-8. [DOI: 10.1039/c6cc04672j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein a simple and practical proline-derived transannular N-cap as a helix nucleating template in diverse bio-related peptide sequences via macrolactamization on resin.
Collapse
Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Jingxu Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Chuan Shi
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Hui Zhao
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering
- Beijing Nuclear Magnetic Resonance Center
- Peking University
- Beijing
- China
| | - Zigang Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| |
Collapse
|
65
|
Kung VM, Cornilescu G, Gellman SH. Impact of Strand Number on Parallel β-Sheet Stability. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
66
|
Takayanagi A, Miyakawa T, Asano A, Ohtsuka J, Tanokura M, Arioka M. Expression, purification, refolding, and enzymatic characterization of two secretory phospholipases A2 from Neurospora crassa. Protein Expr Purif 2015; 115:69-75. [DOI: 10.1016/j.pep.2015.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/06/2015] [Accepted: 08/08/2015] [Indexed: 10/23/2022]
|
67
|
Yang J, Tsutsumi H, Furuta T, Sakurai M, Mihara H. Interaction of amphiphilic α-helical cell-penetrating peptides with heparan sulfate. Org Biomol Chem 2015; 12:4673-81. [PMID: 24867193 DOI: 10.1039/c4ob00673a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-penetrating peptides (CPPs) are able to be taken up by cells and can deliver macromolecular cargos. However, the mechanism of this internalization is not yet fully understood. Recent theories suggest that the binding of cationic CPPs to negatively charged extracellular glycosaminoglycans, such as heparan sulfate (HS), is a possible mechanism of cellular uptake (CU). Our group has screened the CU activities of 54 systematically designed amphiphilic α-helical peptides in HeLa cells. Notably, a mutation in even a single residue significantly alters the CU ability of a peptide. To determine the structure-CU activity relationship of CPPs, four peptides, which contain a difference in one or two amino acids (i.e., Arg/Glu and Ala/Phe), were chosen from our CPP library to examine their interactions with HS. Fluorescence spectroscopy, isothermal titration calorimetry (ITC) and dynamic light scattering analysis indicated that the HS-binding affinities and HS-clustering abilities of the four CPPs correlated well with their CU activities in HeLa and A549 cells. The heat capacities of the CPPs, determined using ITC and binding free energy decomposition analyses in molecular dynamics simulations, revealed that electrostatic interactions were more dominant in the HS-binding processes of Arg-containing peptides in comparison to Glu-containing peptides, whereas hydrophobic contributions were the primary mode of interaction of Phe-containing peptides in comparison to Ala-containing peptides. Furthermore, it was implied that hydrophobic interactions may be more favourable than electrostatic interactions during the CU process.
Collapse
Affiliation(s)
- Ji Yang
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-40, Midori-ku, Yokohama 226-8501, Japan.
| | | | | | | | | |
Collapse
|
68
|
Kung VM, Cornilescu G, Gellman SH. Impact of Strand Number on Parallel β-Sheet Stability. Angew Chem Int Ed Engl 2015; 54:14336-9. [PMID: 26457984 DOI: 10.1002/anie.201506448] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/27/2015] [Indexed: 11/10/2022]
Abstract
We have examined whether parallel β-sheet secondary structure becomes more stable as the number of β-strands increases, via comparisons among peptides designed to adopt two- or three-stranded parallel β-sheet conformations in aqueous solution. Our three-strand design is the first experimental model of a triple-stranded parallel β-sheet. Analysis of the designed peptides by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy supports the hypothesis that increasing the number of β-strands, from two to three, increases the stability of the parallel β-sheet. We present the first experimental evidence for cooperativity in the folding of a triple-stranded parallel β-sheet, and we show how minimal model systems may enable experimental documentation of characteristic properties, such as CD spectra, of parallel β-sheets.
Collapse
Affiliation(s)
- Vanessa M Kung
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706 (USA)
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706 (USA)
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706 (USA).
| |
Collapse
|
69
|
Follmer C, Coelho-Cerqueira E, Yatabe-Franco DY, Araujo GDT, Pinheiro AS, Domont GB, Eliezer D. Oligomerization and Membrane-binding Properties of Covalent Adducts Formed by the Interaction of α-Synuclein with the Toxic Dopamine Metabolite 3,4-Dihydroxyphenylacetaldehyde (DOPAL). J Biol Chem 2015; 290:27660-79. [PMID: 26381411 DOI: 10.1074/jbc.m115.686584] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 01/15/2023] Open
Abstract
Oxidative deamination of dopamine produces the highly toxic aldehyde 3,4-dihydroxyphenylacetaldehyde (DOPAL), enhanced production of which is found in post-mortem brains of Parkinson disease patients. When injected into the substantia nigra of rat brains, DOPAL causes the loss of dopaminergic neurons accompanied by the accumulation of potentially toxic oligomers of the presynaptic protein α-synuclein (aS), potentially explaining the synergistic toxicity described for dopamine metabolism and aS aggregation. In this work, we demonstrate that DOPAL interacts with aS via formation of Schiff-base and Michael-addition adducts with Lys residues, in addition to causing oxidation of Met residues to Met-sulfoxide. DOPAL modification leads to the formation of small aS oligomers that may be cross-linked by DOPAL. Both monomeric and oligomeric DOPAL adducts potently inhibit the formation of mature amyloid fibrils by unmodified aS. The binding of aS to either lipid vesicles or detergent micelles, which results in a gain of α-helix structure in its N-terminal lipid-binding domain, protects the protein against DOPAL adduct formation and, consequently, inhibits DOPAL-induced aS oligomerization. Functionally, aS-DOPAL monomer exhibits a reduced affinity for small unilamellar vesicles with lipid composition similar to synaptic vesicles, in addition to diminished membrane-induced α-helical content in comparison with the unmodified protein. These results suggest that DOPAL could compromise the functionality of aS, even in the absence of protein oligomerization, by affecting the interaction of aS with lipid membranes and hence its role in the regulation of synaptic vesicle traffic in neurons.
Collapse
Affiliation(s)
- Cristian Follmer
- From the Departments of Physical Chemistry and the Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065
| | | | | | - Gabriel D T Araujo
- Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil and
| | - Anderson S Pinheiro
- Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil and
| | - Gilberto B Domont
- Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil and
| | - David Eliezer
- the Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065
| |
Collapse
|
70
|
Hossain MA, Haugaard-Kedström LM, Rosengren KJ, Bathgate RAD, Wade JD. Chemically synthesized dicarba H2 relaxin analogues retain strong RXFP1 receptor activity but show an unexpected loss of in vitro serum stability. Org Biomol Chem 2015; 13:10895-903. [PMID: 26368576 DOI: 10.1039/c5ob01539a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptides and proteins are now acknowledged as viable alternatives to small molecules as potential therapeutic agents. A primary limitation to their more widespread acceptance is their generally short in vivo half-lives due to serum enzyme susceptibility and rapid renal clearance. Numerous chemical approaches to address this concern have been undertaken in recent years. The replacement of disulfide bonds with non-reducible elements has been demonstrated to be one effective means by eliminating the deleterious effect of serum reductases. In particular, substitution with dicarba bonds via ring closure metathesis has been increasingly applied to many bioactive cystine-rich peptides. We used this approach for the replacement of the A-chain intramolecular disulfide bond of human relaxin 2 (H2 relaxin), an insulin-like peptide that has important regulatory roles in cardiovascular and connective tissue homeostasis that has led to successful Phase IIIa clinical trials for the treatment of acute heart failure. Use of efficient solid phase synthesis of the two peptide chains was followed by on-resin ring closure metathesis and formation of the dicarba bond within the A-chain and then by off-resin combination with the B-chain via sequential directed inter-chain disulfide bond formation. After purification and comprehensive chemical characterization, the two isomeric synthetic H2 relaxin analogues were shown to retain near-equipotent RXFP1 receptor binding and activation propensity. Unexpectedly, the in vitro serum stability of the analogues was greatly reduced compared with the native peptide. Circular dichroism spectroscopy studies showed subtle differences in the secondary structures between dicarba analogues and H2 relaxin suggesting that, although the overall fold is retained, it may be destabilized which could account for rapid degradation of dicarba analogues in serum. Caution is therefore recommended when using ring closure metathesis as a general approach to enhance peptide stability.
Collapse
Affiliation(s)
- Mohammed Akhter Hossain
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia.
| | | | | | | | | |
Collapse
|
71
|
Pfefferkorn CM, Walker RL, He Y, Gruschus JM, Lee JC. Tryptophan probes reveal residue-specific phospholipid interactions of apolipoprotein C-III. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2821-8. [PMID: 26301570 DOI: 10.1016/j.bbamem.2015.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 11/27/2022]
Abstract
Apolipoproteins are essential human proteins for lipid metabolism. Together with phospholipids, they constitute lipoproteins, nm to μm sized particles responsible for transporting cholesterol and triglycerides throughout the body. To investigate specific protein-lipid interactions, we produced and characterized three single-Trp containing apolipoprotein C-III (ApoCIII) variants (W42 (W54F/W65F), W54 (W42F/W65F), W65 (W42F/W54F)). Upon binding to phospholipid vesicles, wild-type ApoCIII adopts an α-helical conformation (50% helicity) as determined by circular dichroism spectroscopy with an approximate apparent partition constant of 3×10(4) M(-1). Steady-state and time-resolved fluorescence measurements reveal distinct residue-specific behaviors with W54 experiencing the most hydrophobic environment followed by W42 and W65. Interestingly, time-resolved anisotropy measurements show a converse trend for relative Trp mobility with position 54 being the least immobile. To determine the relative insertion depths of W42, W54, and W65 in the bilayer, fluorescence quenching experiments were performed using three different brominated lipids. W65 had a clear preference for residing near the headgroup while W54 and W42 sample the range of depths ~8-11 Å from the bilayer center. On average, W54 is slightly more embedded than W42. Based on Trp spectral differences between ApoCIII binding to phospholipid vesicles and sodium dodecyl sulfate micelles, we suggest that ApoCIII adopts an alternate helical conformation on the bilayer which could have functional implications.
Collapse
Affiliation(s)
- Candace M Pfefferkorn
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert L Walker
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi He
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M Gruschus
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer C Lee
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
72
|
Sequence, structure, and cooperativity in folding of elementary protein structural motifs. Proc Natl Acad Sci U S A 2015. [PMID: 26216963 DOI: 10.1073/pnas.1506309112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Residue-level unfolding of two helix-turn-helix proteins--one naturally occurring and one de novo designed--is reconstructed from multiple sets of site-specific (13)C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa-Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako-Saitô-Muñoz-Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and (13)C-amide I' bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for "experimental" reaction coordinates--namely, the degree of local folding as sensed by site-specific (13)C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.
Collapse
|
73
|
Jamasbi E, Ciccotosto GD, Tailhades J, Robins-Browne RM, Ugalde CL, Sharples RA, Patil N, Wade JD, Hossain MA, Separovic F. Site of fluorescent label modifies interaction of melittin with live cells and model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2031-9. [PMID: 26051124 DOI: 10.1016/j.bbamem.2015.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 05/30/2015] [Accepted: 06/02/2015] [Indexed: 02/01/2023]
Abstract
The mechanism of membrane disruption by melittin (MLT) of giant unilamellar vesicles (GUVs) and live cells was studied using fluorescence microscopy and two fluorescent synthetic analogues of MLT. The N-terminus of one of these was acylated with thiopropionic acid to enable labeling with maleimido-AlexaFluor 430 to study the interaction of MLT with live cells. It was compared with a second analogue labeled at P14C. The results indicated that the fluorescent peptides adhered to the membrane bilayer of phosphatidylcholine GUVs and inserted into the plasma membrane of HeLa cells. Fluorescence and light microscopy revealed changes in cell morphology after exposure to MLT peptides and showed bleb formation in the plasma membrane of HeLa cells. However, the membrane disruptive effect was dependent upon the location of the fluorescent label on the peptide and was greater when MLT was labeled at the N-terminus. Proline at position 14 appeared to be important for antimicrobial activity, hemolysis and cytotoxicity, but not essential for cell membrane disruption.
Collapse
Affiliation(s)
- Elaheh Jamasbi
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia
| | | | - Julien Tailhades
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, VIC 3010, Australia
| | - Roy M Robins-Browne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3010, Australia; Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Cathryn L Ugalde
- Department of Biochemistry & Molecular Biology, Bio21 Institute, The University of Melbourne, VIC 3010, Australia
| | - Robyn A Sharples
- Department of Biochemistry & Molecular Biology, Bio21 Institute, The University of Melbourne, VIC 3010, Australia
| | - Nitin Patil
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, VIC 3010, Australia
| | - John D Wade
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, VIC 3010, Australia
| | - Mohammed Akhter Hossain
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, VIC 3010, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia
| |
Collapse
|
74
|
|
75
|
Ysselstein D, Joshi M, Mishra V, Griggs AM, Asiago JM, McCabe GP, Stanciu LA, Post CB, Rochet JC. Effects of impaired membrane interactions on α-synuclein aggregation and neurotoxicity. Neurobiol Dis 2015; 79:150-63. [PMID: 25931201 DOI: 10.1016/j.nbd.2015.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 01/08/2023] Open
Abstract
The post-mortem brains of individuals with Parkinson's disease (PD) and other synucleinopathy disorders are characterized by the presence of aggregated forms of the presynaptic protein α-synuclein (aSyn). Understanding the molecular mechanism of aSyn aggregation is essential for the development of neuroprotective strategies to treat these diseases. In this study, we examined how interactions between aSyn and phospholipid vesicles influence the protein's aggregation and toxicity to dopaminergic neurons. Two-dimensional NMR data revealed that two familial aSyn mutants, A30P and G51D, populated an exposed, membrane-bound conformer in which the central hydrophobic region was dissociated from the bilayer to a greater extent than in the case of wild-type aSyn. A30P and G51D had a greater propensity to undergo membrane-induced aggregation and elicited greater toxicity to primary dopaminergic neurons compared to the wild-type protein. In contrast, the non-familial aSyn mutant A29E exhibited a weak propensity to aggregate in the presence of phospholipid vesicles or to elicit neurotoxicity, despite adopting a relatively exposed membrane-bound conformation. Our findings suggest that the aggregation of exposed, membrane-bound aSyn conformers plays a key role in the protein's neurotoxicity in PD and other synucleinopathy disorders.
Collapse
Affiliation(s)
- Daniel Ysselstein
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Mehul Joshi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Vartika Mishra
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Amy M Griggs
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Josephat M Asiago
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - George P McCabe
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Lia A Stanciu
- Schools of Materials Engineering and Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
76
|
Takechi-Haraya Y, Tanaka K, Tsuji K, Asami Y, Izawa H, Shigenaga A, Otaka A, Saito H, Kawakami K. Molecular Complex Composed of β-Cyclodextrin-Grafted Chitosan and pH-Sensitive Amphipathic Peptide for Enhancing Cellular Cholesterol Efflux under Acidic pH. Bioconjug Chem 2015; 26:572-81. [DOI: 10.1021/acs.bioconjchem.5b00037] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yuki Takechi-Haraya
- Institute
of Health Biosciences, Graduate School of Pharmaceutical Sciences, The University of Tokushima, 1-78-1 Shoumachi, Tokushima 770-8505, Japan
- International
Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Kento Tanaka
- Institute
of Health Biosciences, Graduate School of Pharmaceutical Sciences, The University of Tokushima, 1-78-1 Shoumachi, Tokushima 770-8505, Japan
| | - Kohei Tsuji
- Institute
of Health Biosciences, Graduate School of Pharmaceutical Sciences, The University of Tokushima, 1-78-1 Shoumachi, Tokushima 770-8505, Japan
| | - Yasuo Asami
- TA Instruments Japan, Inc., 5-2-4 Nishi-Gotanda, Shinagawa-ku, Tokyo, 141-0031 Japan
| | - Hironori Izawa
- International
Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
| | - Akira Shigenaga
- Institute
of Health Biosciences, Graduate School of Pharmaceutical Sciences, The University of Tokushima, 1-78-1 Shoumachi, Tokushima 770-8505, Japan
| | - Akira Otaka
- Institute
of Health Biosciences, Graduate School of Pharmaceutical Sciences, The University of Tokushima, 1-78-1 Shoumachi, Tokushima 770-8505, Japan
| | - Hiroyuki Saito
- Institute
of Health Biosciences, Graduate School of Pharmaceutical Sciences, The University of Tokushima, 1-78-1 Shoumachi, Tokushima 770-8505, Japan
| | - Kohsaku Kawakami
- International
Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| |
Collapse
|
77
|
Baker EG, Bartlett GJ, Crump MP, Sessions RB, Linden N, Faul CFJ, Woolfson DN. Local and macroscopic electrostatic interactions in single α-helices. Nat Chem Biol 2015; 11:221-8. [PMID: 25664692 PMCID: PMC4668598 DOI: 10.1038/nchembio.1739] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/01/2014] [Indexed: 11/09/2022]
Abstract
The noncovalent forces that stabilize protein structures are not fully understood. One way to address this is to study equilibria between unfolded states and α-helices in peptides. Electrostatic forces-which include interactions between side chains, the backbone and side chains, and side chains and the helix macrodipole-are believed to contribute to these equilibria. Here we probe these interactions experimentally using designed peptides. We find that both terminal backbone-side chain and certain side chain-side chain interactions (which include both local effects between proximal charges and interatomic contacts) contribute much more to helix stability than side chain-helix macrodipole electrostatics, which are believed to operate at larger distances. This has implications for current descriptions of helix stability, the understanding of protein folding and the refinement of force fields for biomolecular modeling and simulations. In addition, this study sheds light on the stability of rod-like structures formed by single α-helices, which are common in natural proteins such as non-muscle myosins.
Collapse
Affiliation(s)
- Emily G. Baker
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Richard B. Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Noah Linden
- School of Mathematics, University of Bristol, University Walk, Bristol, BS8 1TW, UK
| | - Charl F. J. Faul
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| |
Collapse
|
78
|
Smaldone G, Diana D, Pollegioni L, Di Gaetano S, Fattorusso R, Pedone E. Insight into conformational modification of alpha-synuclein in the presence of neuronal whole cells and of their isolated membranes. FEBS Lett 2015; 589:798-804. [DOI: 10.1016/j.febslet.2015.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/30/2015] [Accepted: 02/10/2015] [Indexed: 10/24/2022]
|
79
|
Thermal expansivities of peptides, polypeptides and proteins as measured by pressure perturbation calorimetry. Methods 2015; 76:61-66. [PMID: 25602591 DOI: 10.1016/j.ymeth.2015.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/06/2015] [Accepted: 01/07/2015] [Indexed: 11/23/2022] Open
Abstract
The main goal of this work was to provide direct experimental evidence that the expansivity of peptides, polypeptides and proteins as measured by pressure perturbation calorimetry (PPC), can serve as a proxy to characterize relative compactness of proteins, especially the denatured state ensemble. This is very important as currently only small angle X-ray scattering (SAXS), intrinsic viscosity and, to a lesser degree, fluorescence resonance transfer (FRET) experiments are capable of reporting on the compactness of denatured state ensembles. We combined the expansivity measurements with other biophysical methods (far-UV circular dichroism spectroscopy, differential scanning calorimetry, and small angle X-ray scattering). Three case studies of the effects of conformational changes on the expansivity of polypeptides in solution are presented. We have shown that expansivity appears to be insensitive to the helix-coil transition, and appears to reflect the changes in hydration of the side-chains. We also observed that the expansivity is sensitive to the global conformation of the polypeptide chain and thus can be potentially used to probe hydration of different collapsed states of denatured or even intrinsically disordered proteins.
Collapse
|
80
|
Xiao C, Pérez LM, Russell DH. Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions. Analyst 2015; 140:6933-44. [DOI: 10.1039/c5an00826c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The factors affecting conformational preference of gas phase peptide ions are investigated by IM-MS and molecular dynamics simulation.
Collapse
Affiliation(s)
- Chunying Xiao
- Texas A&M University
- Department of Chemistry
- College Station
- USA
| | - Lisa M. Pérez
- Texas A&M University
- Department of Chemistry
- College Station
- USA
| | | |
Collapse
|
81
|
Luth ES, Bartels T, Dettmer U, Kim NC, Selkoe DJ. Purification of α-synuclein from human brain reveals an instability of endogenous multimers as the protein approaches purity. Biochemistry 2014; 54:279-92. [PMID: 25490121 PMCID: PMC4303315 DOI: 10.1021/bi501188a] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Despite
two decades of research, the structure–function
relationships of endogenous, physiological forms of α-synuclein
(αSyn) are not well understood. Most in vitro studies of this
Parkinson’s disease-related protein have focused on recombinant
αSyn that is unfolded and monomeric, assuming that this represents
its state in the normal human brain. Recently, we have provided evidence
that αSyn exists in considerable part in neurons, erythrocytes,
and other cells as a metastable multimer that principally sizes as
a tetramer. In contrast to recombinant αSyn, physiological tetramers
purified from human erythrocytes have substantial α-helical
content and resist pathological aggregation into β-sheet rich
fibers. Here, we report the first method to fully purify soluble αSyn
from the most relevant source, human brain. We describe protocols
that purify αSyn to homogeneity from nondiseased human cortex
using ammonium sulfate precipitation, gel filtration, and ion exchange,
hydrophobic interaction, and affinity chromatographies. Cross-linking
of the starting material and the partially purified chromatographic
fractions revealed abundant αSyn multimers, including apparent
tetramers, but these were destabilized in large part to monomers during
the final purification step. The method also fully purified the homologue
β-synuclein, with a similar outcome. Circular dichroism spectroscopy
showed that purified, brain-derived αSyn can display more helical
content than the recombinant protein, but this result varied. Collectively,
our data suggest that purifying αSyn to homogeneity destabilizes
native, α-helix-rich multimers that exist in intact and partially
purified brain samples. This finding suggests existence of a stabilizing
cofactor (e.g., a small lipid) present inside neurons that is lost
during final purification.
Collapse
Affiliation(s)
- Eric S Luth
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School , Boston, Massachusetts 02115, United States
| | | | | | | | | |
Collapse
|
82
|
Jamasbi E, Batinovic S, Sharples RA, Sani MA, Robins-Browne RM, Wade JD, Separovic F, Hossain MA. Melittin peptides exhibit different activity on different cells and model membranes. Amino Acids 2014; 46:2759-66. [DOI: 10.1007/s00726-014-1833-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 08/26/2014] [Indexed: 11/30/2022]
|
83
|
N-alpha-acetylation of α-synuclein increases its helical folding propensity, GM1 binding specificity and resistance to aggregation. PLoS One 2014; 9:e103727. [PMID: 25075858 PMCID: PMC4116227 DOI: 10.1371/journal.pone.0103727] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/05/2014] [Indexed: 12/02/2022] Open
Abstract
A switch in the conformational properties of α-synuclein (αS) is hypothesized to be a key step in the pathogenic mechanism of Parkinson’s disease (PD). Whereas the beta-sheet-rich state of αS has long been associated with its pathological aggregation in PD, a partially alpha-helical state was found to be related to physiological lipid binding; this suggests a potential role of the alpha-helical state in controlling synaptic vesicle cycling and resistance to β-sheet rich aggregation. N-terminal acetylation is the predominant post-translational modification of mammalian αS. Using circular dichroism, isothermal titration calorimetry, and fluorescence spectroscopy, we have analyzed the effects of N-terminal acetylation on the propensity of recombinant human αS to form the two conformational states in interaction with lipid membranes. Small unilamellar vesicles of negatively charged lipids served as model membranes. Consistent with previous NMR studies using phosphatidylserine, we found that membrane-induced α-helical folding was enhanced by N-terminal acetylation and that greater exothermic heat could be measured upon vesicle binding of the modified protein. Interestingly, the folding and lipid binding enhancements with phosphatidylserine in vitro were weak when compared to that of αS with GM1, a lipid enriched in presynaptic membranes. The resultant increase in helical folding propensity of N-acetylated αS enhanced its resistance to aggregation. Our findings demonstrate the significance of the extreme N-terminus for folding nucleation, for relative GM1 specificity of αS-membrane interaction, and for a protective function of N-terminal-acetylation against αS aggregation mediated by GM1.
Collapse
|
84
|
Kaplan JB, Reinke AW, Keating AE. Increasing the affinity of selective bZIP-binding peptides through surface residue redesign. Protein Sci 2014; 23:940-53. [PMID: 24729132 PMCID: PMC4088978 DOI: 10.1002/pro.2477] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 12/11/2022]
Abstract
The coiled-coil dimer is a prevalent protein interaction motif that is important for many cellular processes. The basic leucine-zipper (bZIP) transcription factors are one family of proteins for which coiled-coil mediated dimerization is essential for function, and misregulation of bZIPs can lead to disease states including cancer. This makes coiled coils attractive protein-protein interaction targets to disrupt using engineered molecules. Previous work designing peptides to compete with native coiled-coil interactions focused primarily on designing the core residues of the interface to achieve affinity and specificity. However, folding studies on the model bZIP GCN4 show that coiled-coil surface residues also contribute to binding affinity. Here we extend a prior study in which peptides were designed to bind tightly and specifically to representative members of each of 20 human bZIP families. These "anti-bZIP" peptides were designed with an emphasis on target-binding specificity, with contributions to design-target specificity and affinity engineered considering only the coiled-coil core residues. High-throughput testing using peptide arrays indicated many successes. We have now measured the binding affinities and specificities of anti-bZIPs that bind to FOS, XBP1, ATF6, and CREBZF in solution and tested whether redesigning the surface residues can increase design-target affinity. Incorporating residues that favor helix formation into the designs increased binding affinities in all cases, providing low-nanomolar binders of each target. However, changes in surface electrostatic interactions sometimes changed the binding specificity of the designed peptides.
Collapse
Affiliation(s)
- Jenifer B Kaplan
- Department of Biology, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Aaron W Reinke
- Department of Biology, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
- Division of Biological Sciences, University of California San DiegoLa Jolla, California, 92093
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| |
Collapse
|
85
|
Rouch DA. Evolution of the first genetic cells and the universal genetic code: a hypothesis based on macromolecular coevolution of RNA and proteins. J Theor Biol 2014; 357:220-44. [PMID: 24931677 DOI: 10.1016/j.jtbi.2014.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022]
Abstract
A qualitative hypothesis based on coevolution of protein and nucleic acid macromolecules was developed to explain the evolution of the first genetic cells, from the likely organic chemical-rich environment of early earth, through to the Last Universal Common Ancestor (LUCA). The evolution of the first genetic cell was divided into three phases, proto-genetic cells I, II and III, and the transition to each milestone is described, based on development of chemical cross-catalysis, bio-cross-catalysis, and the universal genetic code, respectively. Selection of macromolecular properties of both peptides and nucleic acids, in response to environmental factors, was likely to be a key aspect of early evolution. The development of hereditable nucleic acids with various key functions; translation, transcription and replication, is described. These functions are envisaged to have coevolved with protein enzymes, from simple organic precursors. Genetically heritable nucleotides may have developed after the local earth environment had cooled below 63 °C. Around this temperature G-C bases would have been preferentially utilized for nucleotide synthesis. Under these conditions RNA type nucleotides were then likely selected from a range of different types of nucleotide backbones through template-based synthesis. Initial development of the genetic coding system was simplified by the availability of proto-messenger RNA sequences that contained only G and C bases, and the need to encode only four amino acids. The step-wise addition of further amino acids to the code was predicted to parallel the growing metabolic complexity of the proto-genetic cell. On completion of this evolutionary process the proto-genetic cell is envisaged to have become the LUCA, the last common ancestor of bacteria, eukaryote and archaea domains. Key issues addressed by the model include: (a) the transition from non-hereditable random sequences of peptides and nucleic acids to specific proteins coded by hereditable nucleotide sequences, (b) the origin of homochiral amino acids and sugars, and (c) the mutation limits on the sizes of early nucleic acid genomes. The first genome was limited to a size of about 200 base pairs.
Collapse
Affiliation(s)
- Duncan A Rouch
- Biotechnology and Environmental Biology, RMIT University, PO Box 71, Bundoora, Melbourne, Vic 3083, Australia.
| |
Collapse
|
86
|
Stefanovic AND, Stöckl MT, Claessens MMAE, Subramaniam V. α-Synuclein oligomers distinctively permeabilize complex model membranes. FEBS J 2014; 281:2838-50. [PMID: 24767583 DOI: 10.1111/febs.12824] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/16/2014] [Accepted: 04/23/2014] [Indexed: 11/30/2022]
Abstract
α-Synuclein oligomers are increasingly considered to be responsible for the death of dopaminergic neurons in Parkinson's disease. The toxicity mechanism of α-synuclein oligomers likely involves membrane permeabilization. Even though it is well established that α-synuclein oligomers bind and permeabilize vesicles composed of negatively-charged lipids, little attention has been given to the interaction of oligomers with bilayers of physiologically relevant lipid compositions. We investigated the interaction of α-synuclein with bilayers composed of lipid mixtures that mimic the composition of plasma and mitochondrial membranes. In the present study, we show that monomeric and oligomeric α-synuclein bind to these membranes. The resulting membrane leakage differs from that observed for simple artificial model bilayers. Although the addition of oligomers to negatively-charged lipid vesicles displays fast content release in a bulk permeabilization assay, adding oligomers to vesicles with compositions mimicking mitochondrial membranes shows a much slower loss of content. Oligomers are unable to induce leakage in the artificial plasma membranes, even after long-term incubation. CD experiments indicate that binding to lipid bilayers initially induces conformational changes in both oligomeric and monomeric α-synuclein, which show little change upon long-term incubation of oligomers with membranes. The results of the present study demonstrate that the mitochondrial model membranes are more vulnerable to permeabilization by oligomers than model plasma membranes reconstituted from brain-derived lipids; this preference may imply that increasingly complex membrane components, such as those in the plasma membrane mimic used in the present study, are less vulnerable to damage by oligomers.
Collapse
Affiliation(s)
- Anja N D Stefanovic
- Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine and MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
| | | | | | | |
Collapse
|
87
|
Wiedman G, Fuselier T, He J, Searson PC, Hristova K, Wimley WC. Highly efficient macromolecule-sized poration of lipid bilayers by a synthetically evolved peptide. J Am Chem Soc 2014; 136:4724-31. [PMID: 24588399 PMCID: PMC3985440 DOI: 10.1021/ja500462s] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Indexed: 12/30/2022]
Abstract
Peptides that self-assemble, at low concentration, into bilayer-spanning pores which allow the passage of macromolecules would be beneficial in multiple areas of biotechnology. However, there are few, if any, natural or designed peptides that have this property. Here we show that the 26-residue peptide "MelP5", a synthetically evolved gain-of-function variant of the bee venom lytic peptide melittin identified in a high-throughput screen for small molecule leakage, enables the passage of macromolecules across bilayers under conditions where melittin and other pore-forming peptides do not. In surface-supported bilayers, MelP5 forms unusually high conductance, equilibrium pores at peptide:lipid ratios as low as 1:25000. The increase in bilayer conductance due to MelP5 is dramatically higher, per peptide, than the increase due to the parent sequence of melittin or other peptide pore formers. Here we also develop two novel assays for macromolecule leakage from vesicles, and we use them to characterize MelP5 pores in bilayers. We show that MelP5 allows the passage of macromolecules across vesicle membranes at peptide:lipid ratios as low as 1:500, and under conditions where neither osmotic lysis nor gross vesicle destabilization occur. The macromolecule-sized, equilibrium pores formed by MelP5 are unique as neither melittin nor other pore-forming peptides release macromolecules significantly under the same conditions. MelP5 thus appears to belong to a novel functional class of peptide that could form the foundation of multiple potential biotechnological applications.
Collapse
Affiliation(s)
- Gregory Wiedman
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Taylor Fuselier
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Jing He
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Peter C. Searson
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kalina Hristova
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - William C. Wimley
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| |
Collapse
|
88
|
Rahman MA, Kristiansen PE, Veiseth SV, Andersen JT, Yap KL, Zhou MM, Sandlie I, Thorstensen T, Aalen RB. The arabidopsis histone methyltransferase SUVR4 binds ubiquitin via a domain with a four-helix bundle structure. Biochemistry 2014; 53:2091-100. [PMID: 24625295 DOI: 10.1021/bi401436h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In eukaryotes, different chromatin states facilitate or repress gene expression and restrict the activity of transposable elements. Post-translational modifications (PTMs) of amino acid residues on the N-terminal tails of histones are suggested to define such states. The histone lysine methyltransferase (HKMTase) SU(VAR)3-9 RELATED4 (SUVR4) of Arabidopsis thaliana functions as a repressor of transposon activity. Binding of ubiquitin by the WIYLD domain facilitates the addition of two methyl groups to monomethylated lysine 9 of histone H3. By using nuclear magnetic resonance (NMR) spectroscopy, we identified SUVR4 WIYLD (S4WIYLD) as a domain with a four-helix bundle structure, in contrast to three-helix bundles of other ubiquitin binding domains. NMR titration analyses showed that residues of helix α1 (Q38, L39, and D40) and helix α4 (N68, T70, A71, V73, D74, I76, S78, and E82) of S4WIYLD and residues between the first and second β-strands (T9 and G10) and on β-strands 3 (R42, G47, K48, and Q49) and 4 (H68, R72, and L73) undergo significant chemical shift changes when the two proteins interact. A model of the complex, generated using HADDOCK, suggests that the N-terminal and C-terminal parts of S4WIYLD constitute a surface that interacts with charged residues close to the hydrophobic patch of ubiquitin. The WIYLD domains of the closely related SUVR1 and SUVR2 Arabidopsis proteins also bind ubiquitin, indicating that this is a general feature of this domain. The question of whether SUVR proteins act as both readers of monoubiquitinated H2B and writers of histone PTMs is discussed.
Collapse
|
89
|
Zangi R. Side-chain-side-chain interactions and stability of the helical state. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:012723. [PMID: 24580273 DOI: 10.1103/physreve.89.012723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Indexed: 06/03/2023]
Abstract
Understanding the driving forces that lead to the stability of the secondary motifs found in proteins, namely α-helix and β-sheet, is a major goal in structural biology. The thermodynamic stability of these repetitive units is a result of a delicate balance between many factors, which in addition to the peptide chain involves also the solvent. Despite the fact that the backbones of all amino acids are the same (except of that of proline), there are large differences in the propensity of the different amino acids to promote the helical structure. In this paper, we investigate by explicit-solvent molecular dynamics simulations the role of the side chains (modeled as coarse-grained single sites) in stabilizing α helices in an aqueous solution. Our model systems include four (six-mer-nine-mer) peptide lengths in which the magnitude of the effective attraction between the side chains is systematically increased. We find that these interactions between the side chains can induce (for the nine-mer almost completely) a transition from a coil to a helical state. This transition is found to be characterized by three states in which the intermediate state is a partially folded α-helical conformation. In the absence of any interactions between the side chains the free energy change for helix formation has a small positive value indicating that favorable contributions from the side chains are necessary to stabilize the helical conformation. Thus, the helix-coil transition is controlled by the effective potentials between the side-chain residues and the magnitude of the required attraction per residue, which is on the order of the thermal energy, reduces with the length of the peptide. Surprisingly, the plots of the population of the helical state (or the change in the free energy for helix formation) as a function of the total effective interactions between the side chains in the helical state for all peptide lengths fall on the same curve.
Collapse
Affiliation(s)
- Ronen Zangi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain and IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
| |
Collapse
|
90
|
Shabanpoor F, Bathgate RAD, Wade JD, Hossain MA. C-terminus of the B-chain of relaxin-3 is important for receptor activity. PLoS One 2013; 8:e82567. [PMID: 24349312 PMCID: PMC3859608 DOI: 10.1371/journal.pone.0082567] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/24/2013] [Indexed: 01/23/2023] Open
Abstract
Human relaxin-3 is a neuropeptide that is structurally similar to human insulin with two chains (A and B) connected by three disulfide bonds. It is expressed primarily in the brain and has modulatory roles in stress and anxiety, feeding and metabolism, and arousal and behavioural activation. Structure-activity relationship studies have shown that relaxin-3 interacts with its cognate receptor RXFP3 primarily through its B-chain and that its A-chain does not have any functional role. In this study, we have investigated the effect of modification of the B-chain C-terminus on the binding and activity of the peptide. We have chemically synthesised and characterized H3 relaxin as C-termini acid (both A and B chains having free C-termini; native form) and amide forms (both chains’ C-termini were amidated). We have confirmed that the acid form of the peptide is more potent than its amide form at both RXFP3 and RXFP4 receptors. We further investigated the effects of amidation at the C-terminus of individual chains. We report here for the first time that amidation at the C-terminus of the B-chain of H3 relaxin leads to significant drop in the binding and activity of the peptide at RXFP3/RXFP4 receptors. However, modification of the A-chain C-terminus does not have any effect on the activity. We have confirmed using circular dichroism spectroscopy that there is no secondary structural change between the acid and amide form of the peptide, and it is likely that it is the local C-terminal carboxyl group orientation that is crucial for interacting with the receptors.
Collapse
Affiliation(s)
- Fazel Shabanpoor
- Florey Institute for Neuroscience & Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
| | - Ross A. D. Bathgate
- Florey Institute for Neuroscience & Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - John D. Wade
- Florey Institute for Neuroscience & Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (MAH); (JDW)
| | - Mohammed Akhter Hossain
- Florey Institute for Neuroscience & Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (MAH); (JDW)
| |
Collapse
|
91
|
Truncated and constrained helical analogs of antimicrobial esculentin-2EM. Bioorg Med Chem Lett 2013; 23:6717-20. [DOI: 10.1016/j.bmcl.2013.10.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/07/2013] [Accepted: 10/18/2013] [Indexed: 11/30/2022]
|
92
|
Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy. Proc Natl Acad Sci U S A 2013; 110:17314-9. [PMID: 24106309 DOI: 10.1073/pnas.1311876110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The relaxation of helical structures very close to equilibrium is observed via transient 2D IR spectroscopy. An initial distribution of synthetically distorted helices having an unnatural bridge linking the 10th and 12th residues of an alanine-rich α-helix is released to evolve into the equilibrium distribution of α-helix conformations. The bridge constrains the structure to be slightly displaced from the full α-helix equilibrium near these residues, yet the peptide is not unfolded completely. The release is accomplished by a subpicosecond pulse of UV irradiation. The resulting 2D IR signals are used to obtain snapshots of the ∼100-ps helical conformational reorganization of the distorted dihedral angle and distance between amide units at chemical bond length-scale resolution. The decay rates of the angle between the dipoles, dihedral angles, and distance autocorrelations obtained from molecular dynamics simulations support the experiments, providing evidence that the final helix collapse conforms to linear response theory.
Collapse
|
93
|
Kubelka J. Multivariate Analysis of Spectral Data with Frequency Shifts: Application to Temperature Dependent Infrared Spectra of Peptides and Proteins. Anal Chem 2013; 85:9588-95. [DOI: 10.1021/ac402083p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Kubelka
- Department
of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| |
Collapse
|
94
|
Ioannou F, Leontidis E, Archontis G. Helix Formation by Alanine-Based Peptides in Pure Water and Electrolyte Solutions: Insights from Molecular Dynamics Simulations. J Phys Chem B 2013; 117:9866-76. [DOI: 10.1021/jp406231g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Filippos Ioannou
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Epameinondas Leontidis
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Georgios Archontis
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| |
Collapse
|
95
|
|
96
|
Chen C, Huang Y, Ji X, Xiao Y. Efficiently finding the minimum free energy path from steepest descent path. J Chem Phys 2013; 138:164122. [DOI: 10.1063/1.4799236] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
97
|
Olivares-Quiroz L. Thermodynamics of ideal proteinogenic homopolymer chains as a function of the energy spectrum E, helical propensity ω and enthalpic energy barrier. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:155103. [PMID: 23515207 DOI: 10.1088/0953-8984/25/15/155103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A reformulation and generalization of the Zwanzig model (ZW model) for ideal homopolymer chains poly-X, where X represents any of the twenty naturally occurring proteinogenic amino acid residues is presented. This reformulation and generalization provides a direct connection between coarse-grained parameters originally proposed in the ZW model with variables from the Lifson-Roig (LR) theory, such as the helical propensity per residue ω, and new variables introduced here, such as the energy gap Δ between unfolded and folded structures, as well as the ratio f of the energy scales involved. This enables us to discover the relevance of the energy spectrum E to the onset of configurational phase transitions. From the configurational partition function Q, thermodynamic properties such as the configurational entropy S, specific heat v and average energy <E> are calculated in terms of the number of residues K, temperature T, helical propensity ω and energy barrier ΔH for different poly-X chains in vacuo. Results obtained here provide substantial evidence that configurational phase transitions for ideal poly-X chains correspond to first-order phase transitions. An anomalous behavior of the thermodynamic functions <E>, Cv, S with respect to the number K of residues is also highlighted. On-going methods of solution are outlined.
Collapse
Affiliation(s)
- L Olivares-Quiroz
- Universidad Autónoma de la Ciudad de México, Campus Cuautepec, Av La Corona 320, Col Loma Alta CP 07160 DF, Mexico.
| |
Collapse
|
98
|
Balakrishnan VS, Vad BS, Otzen DE. Novicidin's membrane permeabilizing activity is driven by membrane partitioning but not by helicity: a biophysical study of the impact of lipid charge and cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:996-1002. [PMID: 23562965 DOI: 10.1016/j.bbapap.2013.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/05/2013] [Accepted: 03/25/2013] [Indexed: 12/11/2022]
Abstract
We have investigated the interactions between the antimicrobial peptide Novicidin (Nc) and vesicles containing the phospholipid DOPC, with various amounts of DOPG and cholesterol using circular dichroism spectroscopy, calcein release, equilibrium dialysis and isothermal titration calorimetry. Nc adopts a random coil structure in the absence of lipids and in the presence of vesicles containing 100% DOPC. Lipids with 25-40% DOPG induce the highest level of helicity in Nc; higher DOPG levels lead to lower helicity levels and an altered tertiary arrangement of the peptide. However, the ability of Nc to permeabilize vesicles correlates not with helicity but rather with its overall membrane affinity, which is enthalpically favorable but opposed by entropy. Permeabilization declines with increasing mole percentage PG. Changes in helicity correlate with changes in enthalpy, reflecting the enthalpy of helix formation, but not with affinity. There is also a large favorable enthalpic interaction between Nc and lipids in the absence of negative charge and structural changes. Cholesterol slightly reduces membrane permeabilization but has little effect on Nc affinity and secondary structure, and probably protects the membrane by inducing the liquid ordered state. We conclude that helicity is not a prerequisite for activity, and charge-charge interactions are not the only major driving force for AMP interactions with membranes. Our data are compatible with a model in which a superficial binding mode with a large membrane surface binding area per peptide is more efficient than a more intimate embedding within the membrane environment.
Collapse
Affiliation(s)
- Vijay S Balakrishnan
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | | |
Collapse
|
99
|
Balamurugan K, Subramanian V. Length-dependent stability of α-helical peptide upon adsorption to single-walled carbon nanotube. Biopolymers 2013; 99:357-69. [DOI: 10.1002/bip.22185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 09/19/2012] [Accepted: 11/08/2012] [Indexed: 01/12/2023]
Affiliation(s)
- Kanagasabai Balamurugan
- Chemical Laboratory; CSIR-Central Leather Research Institute; Adyar, Chennai; 600 020; India
| | - Venkatesan Subramanian
- Chemical Laboratory; CSIR-Central Leather Research Institute; Adyar, Chennai; 600 020; India
| |
Collapse
|
100
|
Chemical synthesis and orexigenic activity of rat/mouse relaxin-3. Amino Acids 2013; 44:1529-36. [PMID: 23456488 DOI: 10.1007/s00726-013-1478-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
The insulin-like peptide, relaxin-3 was first identified just a decade ago via a genomic database search and is now recognized to be a key neuropeptide with several roles including the regulation of arousal, stress responses and neuroendocrine homeostasis. It also has significant potential as a drug to treat stress and obesity. Its actions are mediated via its cognate G protein-coupled receptor, RXFP3, which is found in abundant numbers in the brain. However, much remains to be determined with respect to the mechanism of neurological action of this peptide. Consequently, the chemical synthesis of the rat and mouse (which share identical primary structures) two-chain, three disulfide peptide was undertaken and the resulting peptide subjected to detailed in vitro and in vivo assay. Use of efficient solid-phase synthesis methods provided the two regioselectively S-protected A- and B-chains which were readily combined via sequential disulfide bond formation. The synthetic rat/mouse relaxin-3 was obtained in high purity and good overall yield. It demonstrated potent orexigenic activity in rats in that central intracerebroventricular infusion led to significantly increased food intake and water drinking.
Collapse
|