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Meloni SL, Matsika S. Theoretical studies of the excited states of p-cyanophenylalanine and comparisons with the natural amino acids phenylalanine and tyrosine. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1497-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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52
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Pazos IM, Ghosh A, Tucker MJ, Gai F. Ester Carbonyl Vibration as a Sensitive Probe of Protein Local Electric Field. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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53
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Markiewicz BN, Yang L, Culik RM, Gao YQ, Gai F. How quickly can a β-hairpin fold from its transition state? J Phys Chem B 2014; 118:3317-25. [PMID: 24611730 PMCID: PMC3969101 DOI: 10.1021/jp500774q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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Understanding the structural nature
of the free energy bottleneck(s)
encountered in protein folding is essential to elucidating the underlying
dynamics and mechanism. For this reason, several techniques, including
Φ-value analysis, have previously been developed to infer the
structural characteristics of such high free-energy or transition
states. Herein we propose that one (or few) appropriately placed backbone
and/or side chain cross-linkers, such as disulfides, could be used
to populate a thermodynamically accessible conformational state that
mimics the folding transition state. Specifically, we test this hypothesis
on a model β-hairpin, Trpzip4, as its folding mechanism has
been extensively studied and is well understood. Our results show
that cross-linking the two β-strands near the turn region increases
the folding rate by an order of magnitude, to about (500 ns)−1, whereas cross-linking the termini results in a hyperstable β-hairpin
that has essentially the same folding rate as the uncross-linked peptide.
Taken together, these findings suggest that cross-linking is not only
a useful strategy to manipulate folding free energy barriers, as shown
in other studies, but also, in some cases, it can be used to stabilize
a folding transition state analogue and allow for direct assessment
of the folding process on the downhill side of the free energy barrier.
The calculated free energy landscape of the cross-linked Trpzip4 also
supports this picture. An empirical analysis further suggests, when
folding of β-hairpins does not involve a significant free energy
barrier, the folding time (τ) follows a power law dependence
on the number of hydrogen bonds to be formed (nH), namely, τ = τ0nHα, with
τ0 = 20 ns and α = 2.3.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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54
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Wu T, Zhang R, Li H, Yang L, Zhuang W. Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: a simulation study. J Chem Phys 2014; 140:055101. [PMID: 24511982 DOI: 10.1063/1.4863562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB(OBC) implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.
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Affiliation(s)
- Tianmin Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Huanhuan Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
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55
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Fazelinia H, Xu M, Cheng H, Roder H. Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c. J Am Chem Soc 2013; 136:733-40. [PMID: 24364692 DOI: 10.1021/ja410437d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two α-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse.
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Affiliation(s)
- Hossein Fazelinia
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
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56
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Culik RM, Annavarapu S, Nanda V, Gai F. Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage. Chem Phys 2013; 422:10.1016/j.chemphys.2013.01.021. [PMID: 24307748 PMCID: PMC3844134 DOI: 10.1016/j.chemphys.2013.01.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Using the miniprotein Trp-cage as a model, we show that D-amino acids can be used to facilitate the delineation of protein folding mechanism. Specifically, we study the folding-unfolding kinetics of three Trp-cage mutants where the native glycine residue near the C-terminus of the α-helix is replaced by a D-amino acid. A previous study showed that these mutations increase the Trp-cage stability, due to a terminal capping effect. Our results show that the stabilizing effect of D-asparagine and D-glutamine originates almost exclusively from a decrease in the unfolding rate, while the D-alanine mutation results in a similar decrease in the unfolding rate, but it also increases the folding rate. Together, these results support a folding mechanism wherein the α-helix formation in the transition state is nucleated at the N-terminus, whereas those long-range native interactions stabilizing this helix are developed at the downhill side of the folding free energy barrier.
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Affiliation(s)
- Robert M. Culik
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Srinivas Annavarapu
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854
| | - Vikas Nanda
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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57
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58
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Lin C, Culik RM, Gai F. Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip. J Am Chem Soc 2013; 135:7668-73. [PMID: 23642153 PMCID: PMC3706100 DOI: 10.1021/ja401473m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein folding involves a large number of sequential molecular steps or conformational substates. Thus, experimental characterization of the underlying folding energy landscape for any given protein is difficult. Herein, we present a new method that can be used to determine the major characteristics of the folding energy landscape in question, e.g., to distinguish between activated and barrierless downhill folding scenarios. This method is based on the idea that the conformational relaxation kinetics of different folding mechanisms at a given final condition will show different dependences on the initial condition. We show, using both simulation and experiment, that it is possible to differentiate between disparate kinetic folding models by comparing temperature jump (T-jump) relaxation traces obtained with a fixed final temperature and varied initial temperatures, which effectively varies the initial potential (VIP) of the system of interest. We apply this method (hereafter refer to as VIPT-jump) to two model systems, tryptophan zipper (Trpzip)-2c and BBL, and our results show that BBL exhibits characteristics of barrierless downhill folding, whereas Trpzip-2c folding encounters a free energy barrier. In addition, using the T-jump data of BBL we are able to provide, via Langevin dynamics simulations, a realistic estimate of its conformational diffusion coefficient.
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Affiliation(s)
- Chun–Wei Lin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert M. Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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59
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Singh S, Chiu CC, Reddy AS, de Pablo JJ. α-helix to β-hairpin transition of human amylin monomer. J Chem Phys 2013; 138:155101. [PMID: 23614446 PMCID: PMC3643982 DOI: 10.1063/1.4798460] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/13/2013] [Indexed: 12/20/2022] Open
Abstract
The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a β-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the β-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the β-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a β-hairpin is an activated process and could constitute the nucleation event for fibril growth.
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Affiliation(s)
- Sadanand Singh
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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60
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Brewster VL, Ashton L, Goodacre R. Monitoring guanidinium-induced structural changes in ribonuclease proteins using Raman spectroscopy and 2D correlation analysis. Anal Chem 2013; 85:3570-5. [PMID: 23463901 DOI: 10.1021/ac303265q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Assessing the stability of proteins by comparing their unfolding profiles is a very important characterization and quality control step for any biopharmaceutical, and this is usually measured by fluorescence spectroscopy. In this paper we propose Raman spectroscopy as a rapid, noninvasive alternative analytical method and we shall show this has enhanced sensitivity and can therefore reveal very subtle protein conformational changes that are not observed with fluorescence measurements. Raman spectroscopy is a powerful nondestructive method that has a strong history of applications in protein characterization. In this work we describe how Raman microscopy can be used as a fast and reliable method of tracking protein unfolding in the presence of a chemical denaturant. We have compared Raman spectroscopic data to the equivalent samples analyzed using fluorescence spectroscopy in order to validate the Raman approach. Calculations from both Raman and fluorescence unfolding curves of [D]50 values and Gibbs free energy correlate well with each other and more importantly agree with the values found in the literature for these proteins. In addition, 2D correlation analysis has been performed on both Raman and fluorescence data sets in order to allow further comparisons of the unfolding behavior indicated by each method. As many biopharmaceuticals are glycosylated in order to be functional, we compare the unfolding profiles of a protein (RNase A) and a glycoprotein (RNase B) as measured by Raman spectroscopy and discuss the implications that glycosylation has on the stability of the protein.
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Affiliation(s)
- Victoria L Brewster
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
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61
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Abstract
To expand the spectroscopic utility of the non-natural amino acid p-cyanophenylalanine (PheCN), we examine the quenching efficiencies of a series of commonly encountered anions toward its fluorescence. We find that iodide exhibits an unusually large Stern-Volmer quenching constant, making it a convenient choice in PheCN fluorescence quenching studies. Indeed, using the villin headpiece subdomain as a testbed we demonstrate that iodide quenching of PheCN fluorescence offers a convenient means to reveal protein conformational heterogeneity. Furthermore, we show that the amino group of PheCN strongly quenches its fluorescence, suggesting that PheCN could be used as a local pH sensor.
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62
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Jangravi Z, Alikhani M, Arefnezhad B, Sharifi Tabar M, Taleahmad S, Karamzadeh R, Jadaliha M, Mousavi SA, Ahmadi Rastegar D, Parsamatin P, Vakilian H, Mirshahvaladi S, Sabbaghian M, Mohseni Meybodi A, Mirzaei M, Shahhoseini M, Ebrahimi M, Piryaei A, Moosavi-Movahedi AA, Haynes PA, Goodchild AK, Nasr-Esfahani MH, Jabbari E, Baharvand H, Sedighi Gilani MA, Gourabi H, Salekdeh GH. A fresh look at the male-specific region of the human Y chromosome. J Proteome Res 2012; 12:6-22. [PMID: 23253012 DOI: 10.1021/pr300864k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Chromosome-centric Human Proteome Project (C-HPP) aims to systematically map the entire human proteome with the intent to enhance our understanding of human biology at the cellular level. This project attempts simultaneously to establish a sound basis for the development of diagnostic, prognostic, therapeutic, and preventive medical applications. In Iran, current efforts focus on mapping the proteome of the human Y chromosome. The male-specific region of the Y chromosome (MSY) is unique in many aspects and comprises 95% of the chromosome's length. The MSY continually retains its haploid state and is full of repeated sequences. It is responsible for important biological roles such as sex determination and male fertility. Here, we present the most recent update of MSY protein-encoding genes and their association with various traits and diseases including sex determination and reversal, spermatogenesis and male infertility, cancers such as prostate cancers, sex-specific effects on the brain and behavior, and graft-versus-host disease. We also present information available from RNA sequencing, protein-protein interaction, post-translational modification of MSY protein-coding genes and their implications in biological systems. An overview of Human Y chromosome Proteome Project is presented and a systematic approach is suggested to ensure that at least one of each predicted protein-coding gene's major representative proteins will be characterized in the context of its major anatomical sites of expression, its abundance, and its functional relevance in a biological and/or medical context. There are many technical and biological issues that will need to be overcome in order to accomplish the full scale mapping.
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Affiliation(s)
- Zohreh Jangravi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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63
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Pazos IM, Gai F. Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability. J Phys Chem B 2012; 116:12473-8. [PMID: 22998405 PMCID: PMC3475735 DOI: 10.1021/jp307414s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
While the thermodynamic effects of trimethylamine oxide (TMAO), urea, and guanidine hydrochloride (GdnHCl) on protein stability are well understood, the underlying mechanisms of action are less well characterized and, in some cases, even under debate. Herein, we employ the stretching vibration of two infrared (IR) reporters, i.e., nitrile (C≡N) and carbonyl (C═O), to directly probe how these cosolvents mediate the ability of water to form hydrogen bonds with the solute of interest, e.g., a peptide. Our results show that these three agents, despite having different effects on protein stability, all act to decrease the strength of the hydrogen bonds formed between water and the infrared probe. While the behavior of TMAO appears to be consistent with its protein-protecting ability, those of urea and GdnHCl are inconsistent with their role as protein denaturants. The latter is of particular interest as it provides strong evidence indicating that although urea and GdnHCl can perturb the hydrogen-bonding property of water their protein-denaturing ability does not arise from a simple indirect mechanism.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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64
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Wang L, Skinner JL. Thermally induced protein unfolding probed by isotope-edited IR spectroscopy. J Phys Chem B 2012; 116:9627-34. [PMID: 22853174 PMCID: PMC3463243 DOI: 10.1021/jp304613b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infrared (IR) spectroscopy has been widely utilized for the study of protein folding, unfolding, and misfolding processes. We have previously developed a theoretical method for calculating IR spectra of proteins in the amide I region. In this work, we apply this method, in combination with replica-exchange molecular dynamics simulations, to study the equilibrium thermal unfolding transition of the villin headpiece subdomain (HP36). Temperature-dependent IR spectra and spectral densities are calculated. The spectral densities correctly reflect the unfolding conformational changes in the simulation. With the help of isotope labeling, we are able to capture the feature that helix 2 of HP36 loses its secondary structure before global unfolding occurs, in agreement with experiment.
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Affiliation(s)
- Lu Wang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706 USA
| | - James L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706 USA
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65
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Culik RM, Jo H, DeGrado WF, Gai F. Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding. J Am Chem Soc 2012; 134:8026-9. [PMID: 22540162 PMCID: PMC3354031 DOI: 10.1021/ja301681v] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.
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Affiliation(s)
- Robert M Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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