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Protein Science : a Publication of the... Aug 2021This Perspective is intended to raise questions about the conventional interpretation of protein folding. According to the conventional interpretation, developed over...
This Perspective is intended to raise questions about the conventional interpretation of protein folding. According to the conventional interpretation, developed over many decades, a protein population can visit a vast number of conformations under unfolding conditions, but a single dominant native population emerges under folding conditions. Accordingly, folding comes with a substantial loss of conformational entropy. How is this price paid? The conventional answer is that favorable interactions between and among the side chains can compensate for entropy loss, and moreover, these interactions are responsible for the structural particulars of the native conformation. Challenging this interpretation, the Perspective introduces a proposal that high energy (i.e., unfavorable) excluding interactions winnow the accessible population substantially under physical-chemical conditions that favor folding. Both steric clash and unsatisfied hydrogen bond donors and acceptors are classified as excluding interactions, so called because conformers with such disfavored interactions will be largely excluded from the thermodynamic population. Both excluding interactions and solvent factors that induce compactness are somewhat nonspecific, yet together they promote substantial chain organization. Moreover, proteins are built on a backbone scaffold consisting of α-helices and strands of β-sheet, where the number of hydrogen bond donors and acceptors is exactly balanced. These repetitive secondary structural elements are the only two conformers that can be both completely hydrogen-bond satisfied and extended indefinitely without encountering a steric clash. Consequently, the number of fundamental folds is limited to no more than ~10,000 for a protein domain. Once excluding interactions are taken into account, the issue of "frustration" is largely eliminated and the Levinthal paradox is resolved. Putting the "bottom line" at the top: it is likely that hydrogen-bond satisfaction represents a largely under-appreciated parameter in protein folding models.
Topics: Entropy; Hydrogen Bonding; Models, Molecular; Protein Conformation; Protein Folding; Proteins; Thermodynamics
PubMed: 33938055
DOI: 10.1002/pro.4096 -
Protein Science : a Publication of the... Nov 2016A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free... (Review)
Review
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
Topics: Models, Chemical; Models, Molecular; Protein Folding; Thermodynamics
PubMed: 27522064
DOI: 10.1002/pro.3015 -
Biochemical Society Transactions Feb 2024Membrane proteins play key roles in human health, contributing to cellular signaling, ATP synthesis, immunity, and metabolite transport. Protein folding is the pivotal... (Review)
Review
Membrane proteins play key roles in human health, contributing to cellular signaling, ATP synthesis, immunity, and metabolite transport. Protein folding is the pivotal early step for their proper functioning. Understanding how this class of proteins adopts their native folds could potentially aid in drug design and therapeutic interventions for misfolding diseases. It is an essential piece in the whole puzzle to untangle their kinetic complexities, such as how rapid membrane proteins fold, how their folding speeds are influenced by changing conditions, and what mechanisms are at play. This review explores the folding speed aspect of multipass α-helical membrane proteins, encompassing plausible folding scenarios based on the timing and stability of helix packing interactions, methods for characterizing the folding time scales, relevant folding steps and caveats for interpretation, and potential implications. The review also highlights the recent estimation of the so-called folding speed limit of helical membrane proteins and discusses its consequent impact on the current picture of folding energy landscapes.
Topics: Humans; Membrane Proteins; Protein Structure, Secondary; Protein Folding; Kinetics
PubMed: 38385525
DOI: 10.1042/BST20231315 -
Annual Review of Biophysics Jul 2016Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments... (Review)
Review
Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments over time include the HX pulse labeling method with nuclear magnetic resonance analysis, the fragment separation method, the addition to it of mass spectrometric (MS) analysis, and recent improvements in the HX MS technique and data analysis. Also, the discovery of protein foldons and their role supplies an essential interpretive link. Recent work using HX pulse labeling with MS analysis finds that a number of proteins fold by stepping through a reproducible sequence of native-like intermediates in an ordered pathway. The stepwise nature of the pathway is dictated by the cooperative foldon unit construction of the protein. The pathway order is determined by a sequential stabilization principle; prior native-like structure guides the formation of adjacent native-like structure. This view does not match the funneled energy landscape paradigm of a very large number of folding tracks, which was framed before foldons were known and is more appropriate for the unguided residue-level search to surmount an initial kinetic barrier rather than for the overall unfolded-state to native-state folding pathway.
Topics: Hydrogen; Magnetic Resonance Spectroscopy; Mass Spectrometry; Protein Conformation; Protein Folding; Proteins; Thermodynamics
PubMed: 27145881
DOI: 10.1146/annurev-biophys-062215-011121 -
International Journal of Molecular... Mar 2022Chirality is a universal phenomenon, embracing the space-time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and... (Review)
Review
Chirality is a universal phenomenon, embracing the space-time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.
Topics: Adenosine Triphosphate; Entropy; Peptides; Protein Folding; Proteins; Thermodynamics
PubMed: 35409047
DOI: 10.3390/ijms23073687 -
Current Opinion in Chemical Biology Oct 2021Originally regarded as a disease symptom, amyloids have shown a rich diversity of functions, including biologically beneficial ones. As such, the traditional view of... (Review)
Review
Originally regarded as a disease symptom, amyloids have shown a rich diversity of functions, including biologically beneficial ones. As such, the traditional view of polypeptide aggregation into amyloid-like structures being 'misfolding' should rather be viewed as 'alternative folding.' Various amyloid folds have been recently used to create highly efficient catalysts with specific catalytic efficiencies rivaling those of enzymes. Here we summarize recent developments and applications of catalytic amyloids, derived from both de novo and bioinspired designs, and discuss how progress in the last 2 years reflects on the field as a whole.
Topics: Amyloid; Catalysis; Peptides; Protein Folding
PubMed: 34425319
DOI: 10.1016/j.cbpa.2021.06.010 -
Current Opinion in Structural Biology Feb 2015Many proteins require help from metal cofactors to function properly. Due to the involvement of metal binding, folding of these metalloproteins can be much more... (Review)
Review
Many proteins require help from metal cofactors to function properly. Due to the involvement of metal binding, folding of these metalloproteins can be much more complicated. In recent years, several computational methods have been developed to reveal the essential features of metal-coupled protein folding, ranging from quantum mechanics (QM) to atomistic and coarse-grained (CG) simulations. These theoretical tools have achieved great successes in solving the multiscale difficulties arising from metal binding, and provided new insights into the mechanisms of metalloprotein folding. In this review, we first discuss the interaction features of metal-coordination and then introduce several computational models and their applications in metal-coupled folding. Finally we discuss the effects of metal-binding on the protein energy landscape, which is followed by some perspectives.
Topics: Metals; Models, Molecular; Molecular Dynamics Simulation; Protein Conformation; Protein Folding
PubMed: 25523438
DOI: 10.1016/j.sbi.2014.11.006 -
Current Opinion in Structural Biology Jun 2021Proteins are chief actors in life that perform a myriad of exquisite functions. This diversity has been enabled through the evolution and diversification of protein... (Review)
Review
Proteins are chief actors in life that perform a myriad of exquisite functions. This diversity has been enabled through the evolution and diversification of protein folds. Analysis of sequences and structures strongly suggest that numerous protein pieces have been reused as building blocks and propagated to many modern folds. This information can be traced to understand how the protein world has diversified. In this review, we discuss the latest advances in the analysis of protein evolutionary units, and we use as a model system one of the most abundant and versatile topologies, the TIM-barrel fold, to highlight the existing common principles that interconnect protein evolution, structure, folding, function, and design.
Topics: Amino Acid Sequence; Evolution, Molecular; Protein Folding; Proteins
PubMed: 33453500
DOI: 10.1016/j.sbi.2020.12.007 -
Current Opinion in Structural Biology Aug 2023Structural biology has traditionally focused on the structures of proteins, short nucleic acids, small molecules, and their complexes. However, it is now widely... (Review)
Review
Structural biology has traditionally focused on the structures of proteins, short nucleic acids, small molecules, and their complexes. However, it is now widely recognized that the 3D organization of chromosomes should also be included in this list, despite significant differences in scale and complexity of organization. Here we highlight some notable similarities between the folding processes that shape proteins and chromosomes. Both biomolecules are folded by two types of processes: the affinity-mediated interactions, and by active (ATP-dependent) processes. Both chromosome and proteins in vivo can have partially unstructured and non-equilibrium ensembles with yet to be understood functional roles. By analyzing these biological systems in parallel, we can uncover universal principles of biomolecular organization that transcend specific biopolymers.
Topics: Chromosomes; Protein Folding; Nucleic Acids; Proteins
PubMed: 37327690
DOI: 10.1016/j.sbi.2023.102610 -
The Journal of Physical Chemistry. B Jul 2014Protein folding is a remarkably fast unimolecular reaction, spanning microseconds to hours at room temperature. Thus, free energy differences and activation barriers on... (Review)
Review
Protein folding is a remarkably fast unimolecular reaction, spanning microseconds to hours at room temperature. Thus, free energy differences and activation barriers on the free energy landscape of proteins are rather small. This opens up the possibility of living cells modulating their protein's landscapes, providing cells another way to control the function of their proteomes after transcriptional control, translational control, and post-translational modification. In this Feature Article, we discuss advances in physicochemical studies of protein stability and folding inside living cells. We focus in particular on our studies using fast relaxation imaging (FREI). Although the effect of the cell on protein free energy landscapes is only a few kT, the strong cooperativity of many folding and binding processes allows small modulation of the energy and entropy to produce a large population modulation. Lastly, we discuss some biomolecular processes that are particularly likely to be affected by in-cell modulation of the proteome, and thus of interest for quantitative physical chemistry studies.
Topics: Animals; Cells; Humans; Molecular Imaging; Protein Folding
PubMed: 24878167
DOI: 10.1021/jp501866v