1
|
Duan B, Qiu C, Lockless SW, Sze SH, Kaplan CD. Higher-order epistasis within Pol II trigger loop haplotypes. bioRxiv 2024:2024.01.20.576280. [PMID: 38293233 PMCID: PMC10827151 DOI: 10.1101/2024.01.20.576280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
RNA polymerase II (Pol II) has a highly conserved domain, the trigger loop (TL), that controls transcription fidelity and speed. We previously probed pairwise genetic interactions between residues within and surrounding the TL and identified widespread incompatibility between TLs of different species when placed in the Saccharomyces cerevisiae Pol II context, indicating epistasis between the TL and its surrounding context. We sought to understand the nature of this incompatibility and probe higher order epistasis internal to the TL. We have employed deep mutational scanning with selected natural TL variants ("haplotypes"), and all possible intermediate substitution combinations between them and the yeast Pol II TL. We identified both positive and negative higher-order residue interactions within example TL haplotypes. Intricate higher-order epistasis formed by TL residues was sometimes only apparent from analysis of intermediate genotypes, emphasizing complexity of epistatic interactions. Furthermore, we distinguished TL substitutions with distinct classes of epistatic patterns, suggesting specific TL residues that potentially influence TL evolution. Our examples of complex residue interactions suggest possible pathways for epistasis to facilitate Pol II evolution.
Collapse
Affiliation(s)
- Bingbing Duan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02215
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843
| | - Sing-Hoi Sze
- Department of Computer Science & Engineering, Texas A&M University, College Station, TX 77843
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| |
Collapse
|
2
|
Geng M, Hansanant N, Lu SE, Lockless SW, Shin R, Orugunty R, Smith L. Synthesis and characterization of semisynthetic analogs of the antifungal occidiofungin. Front Microbiol 2022; 13:1056453. [PMID: 36583054 PMCID: PMC9792986 DOI: 10.3389/fmicb.2022.1056453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Occidiofungin is a broad-spectrum antifungal compound produced by Burkholderia contaminans MS14. It is a cyclic glycol-lipopeptide with a novel beta-amino acid (NAA2) containing a hydroxylated C18 fatty acid chain with a xylose sugar. This study reports a strategy to produce semisynthetic analogs of occidiofungin to further explore the structure activity relationships of this class of compounds. Oxidative cleavage of the diol present on carbons five C(5) and six C(6) removes the xylose and twelve carbons of the fatty acid chain. The resulting cyclic peptide product, occidiofungin aldehyde, is devoid of antifungal activity. However, the free aldehyde group on this product can be subjected to reductive amination reactions to provide interesting semisynthetic analogs. This chemistry allows the quick generation of analogs to study the structure activity relationships of this class of compounds. Despite restoring the length of the aliphatic side chain by reductive amination addition with undecylamine or dodecylamine to the free aldehyde group, the obtained analogs did not demonstrate any antifungal activity. The antifungal activity was partially restored by the addition of a DL-dihydrosphingosine. The dodecylamine analog was demonstrated to still bind to the cellular target actin, suggesting that the diol on the side chain of native occidiofungin is important for entry into the cell enabling access to cellular target F-actin. These results show that the alkyl side chain on NAA2 along with the diol present on this side chain is important for occidiofungin's antifungal activity.
Collapse
Affiliation(s)
- Mengxin Geng
- Department of Biology, Texas A&M University, College Station, TX, United States,Sano Chemicals Inc., Bryan, TX, United States
| | - Nopakorn Hansanant
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, United States
| | - Steve W. Lockless
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Ronald Shin
- Central Alabama High-Field NMR Facility, Structural Biology Shared Facility, Cancer Center University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Leif Smith
- Department of Biology, Texas A&M University, College Station, TX, United States,Sano Chemicals Inc., Bryan, TX, United States,*Correspondence: Leif Smith,
| |
Collapse
|
3
|
Gupta R, Rhee KY, Beagle SD, Chawla R, Perdomo N, Lockless SW, Lele PP. Indole modulates cooperative protein-protein interactions in the flagellar motor. PNAS Nexus 2022; 1. [PMID: 35719892 PMCID: PMC9205328 DOI: 10.1093/pnasnexus/pgac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Indole is a major component of the bacterial exometabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant, although they remain poorly understood. Here, we determined how indole modulates the functions of a widely conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum’s direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.
Collapse
Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Kathy Y Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Sarah D Beagle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Ravi Chawla
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Nicolas Perdomo
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| |
Collapse
|
4
|
Abstract
Lead (Pb) is a potent neurotoxin that disrupts synaptic neurotransmission. We report that Synaptotagmin I (SytI), a key regulator of Ca2+-evoked neurotransmitter release, has two high-affinity Pb2+ binding sites that belong to its cytosolic C2A and C2B domains. The crystal structures of Pb2+-complexed C2 domains revealed that protein-bound Pb2+ ions have holodirected coordination geometries and all-oxygen coordination spheres. The on-rate constants of Pb2+ binding to the C2 domains of SytI are comparable to those of Ca2+ and are diffusion-limited. In contrast, the off-rate constants are at least two orders of magnitude smaller, indicating that Pb2+ can serve as both a thermodynamic and kinetic trap for the C2 domains. We demonstrate, using NMR spectroscopy, that population of these sites by Pb2+ ions inhibits further Ca2+ binding despite the existing coordination vacancies. Our work offers a unique insight into the bioinorganic chemistry of Pb(ii) and suggests a mechanism by which low concentrations of Pb2+ ions can interfere with the Ca2+-dependent function of SytI in the cell.
Collapse
Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA.
| | | | | | | | | | | |
Collapse
|
5
|
Abstract
Isothermal titration calorimetry (ITC) is an emerging, label-free technology used to measure ligand binding to membrane proteins. This technology utilizes a titration calorimeter to measure the heat exchange upon ligands binding to proteins, the magnitude of which is based on the overall enthalpy of the reaction. In this protocol, the steps we and others use to measure ion binding to ion transport proteins are described.
Collapse
Affiliation(s)
- Shian Liu
- Department of Biology, Texas A&M University, 3474 TAMU, College Station, TX, 77843-3474, USA
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20148, USA
| | - Steve W Lockless
- Department of Biology, Texas A&M University, 3474 TAMU, College Station, TX, 77843-3474, USA.
| |
Collapse
|
6
|
Shrestha R, Lockless SW, Sorg JA. A Clostridium difficile alanine racemase affects spore germination and accommodates serine as a substrate. J Biol Chem 2017; 292:10735-10742. [PMID: 28487371 DOI: 10.1074/jbc.m117.791749] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/07/2017] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile has become one of the most common bacterial pathogens in hospital-acquired infections in the United States. Although C. difficile is strictly anaerobic, it survives in aerobic environments and transmits between hosts via spores. C. difficile spore germination is triggered in response to certain bile acids and glycine. Although glycine is the most effective co-germinant, other amino acids can substitute with varying efficiencies. Of these, l-alanine is an effective co-germinant and is also a germinant for most bacterial spores. Many endospore-forming bacteria embed alanine racemases into their spore coats, and these enzymes are thought to convert the l-alanine germinant into d-alanine, a spore germination inhibitor. Although the C. difficile Alr2 racemase is the sixth most highly expressed gene during C. difficile spore formation, a previous study reported that Alr2 has little to no role in germination of C. difficile spores in rich medium. Here, we hypothesized that Alr2 could affect C. difficile l-alanine-induced spore germination in a defined medium. We found that alr2 mutant spores more readily germinate in response to l-alanine as a co-germinant. Surprisingly, d-alanine also functioned as a co-germinant. Moreover, we found that Alr2 could interconvert l- and d-serine and that Alr2 bound to l- and d-serine with ∼2-fold weaker affinity to that of l- and d-alanine. Finally, we demonstrate that l- and d-serine are also co-germinants for C. difficile spores. These results suggest that C. difficile spores can respond to a diverse set of amino acid co-germinants and reveal that Alr2 can accommodate serine as a substrate.
Collapse
Affiliation(s)
- Ritu Shrestha
- From the Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Steve W Lockless
- From the Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Joseph A Sorg
- From the Department of Biology, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
7
|
Abstract
There is a growing need to study ligand binding to proteins in native or complex solution using isothermal titration calorimetry (ITC). For example, it is desirable to measure ligand binding to membrane proteins in more native lipid-like environments such as bicelles, where ligands can access both sides of the membrane in a homogeneous environment. A critical step to obtain high signal-to-noise is matching the reaction chamber solution to the ligand solution, typically through a final dialysis or gel filtration step. However, to obtain reproducible bicelles, the lipid concentrations must be carefully controlled which eliminates the use of dialysis that can disrupt these parameters. Here, we report and validate a rapid preparation ITC (RP-ITC) approach to measure ligand binding without the need for a dialysis step. This general approach is used to quantify ion binding to a K(+) channel embedded in bicelles and can be applied to complex, less defined systems.
Collapse
Affiliation(s)
- Xuelin Bian
- Department of Biology, Texas A&M University , 3474 TAMU, College Station, Texas 77843-3474, United States
| | - Steve W Lockless
- Department of Biology, Texas A&M University , 3474 TAMU, College Station, Texas 77843-3474, United States
| |
Collapse
|
8
|
Abstract
The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K(+)-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules.
Collapse
Affiliation(s)
- Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843
| |
Collapse
|
9
|
Mukherjee P, Banerjee S, Wheeler A, Ratliff LA, Irigoyen S, Garcia LR, Lockless SW, Versaw WK. Live imaging of inorganic phosphate in plants with cellular and subcellular resolution. Plant Physiol 2015; 167:628-38. [PMID: 25624397 PMCID: PMC4348774 DOI: 10.1104/pp.114.254003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/25/2015] [Indexed: 05/17/2023]
Abstract
Despite variable and often scarce supplies of inorganic phosphate (Pi) from soils, plants must distribute appropriate amounts of Pi to each cell and subcellular compartment to sustain essential metabolic activities. The ability to monitor Pi dynamics with subcellular resolution in live plants is, therefore, critical for understanding how this essential nutrient is acquired, mobilized, recycled, and stored. Fluorescence indicator protein for inorganic phosphate (FLIPPi) sensors are genetically encoded fluorescence resonance energy transfer-based sensors that have been used to monitor Pi dynamics in cultured animal cells. Here, we present a series of Pi sensors optimized for use in plants. Substitution of the enhanced yellow fluorescent protein component of a FLIPPi sensor with a circularly permuted version of Venus enhanced sensor dynamic range nearly 2.5-fold. The resulting circularly permuted FLIPPi sensor was subjected to a high-efficiency mutagenesis strategy that relied on statistical coupling analysis to identify regions of the protein likely to influence Pi affinity. A series of affinity mutants was selected with dissociation constant values of 0.08 to 11 mm, which span the range for most plant cell compartments. The sensors were expressed in Arabidopsis (Arabidopsis thaliana), and ratiometric imaging was used to monitor cytosolic Pi dynamics in root cells in response to Pi deprivation and resupply. Moreover, plastid-targeted versions of the sensors expressed in the wild type and a mutant lacking the PHOSPHATE TRANSPORT4;2 plastidic Pi transporter confirmed a physiological role for this transporter in Pi export from root plastids. These circularly permuted FLIPPi sensors, therefore, enable detailed analysis of Pi dynamics with subcellular resolution in live plants.
Collapse
Affiliation(s)
- Pallavi Mukherjee
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Swayoma Banerjee
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Amanda Wheeler
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Lyndsay A Ratliff
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Sonia Irigoyen
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - L Rene Garcia
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Wayne K Versaw
- Department of Biology, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
10
|
Liu S, Bian X, Lockless SW. Preferential binding of K+ ions in the selectivity filter at equilibrium explains high selectivity of K+ channels. ACTA ACUST UNITED AC 2012; 140:671-9. [PMID: 23148260 PMCID: PMC3514730 DOI: 10.1085/jgp.201210855] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
K+ channels exhibit strong selectivity for K+ ions over Na+ ions based on electrophysiology experiments that measure ions competing for passage through the channel. During this conduction process, multiple ions interact within the region of the channel called the selectivity filter. Ion selectivity may arise from an equilibrium preference for K+ ions within the selectivity filter or from a kinetic mechanism whereby Na+ ions are precluded from entering the selectivity filter. Here, we measure the equilibrium affinity and selectivity of K+ and Na+ ions binding to two different K+ channels, KcsA and MthK, using isothermal titration calorimetry. Both channels exhibit a large preference for K+ over Na+ ions at equilibrium, in line with electrophysiology recordings of reversal potentials and Ba2+ block experiments used to measure the selectivity of the external-most ion-binding sites. These results suggest that the high selectivity observed during ion conduction can originate from a strong equilibrium preference for K+ ions in the selectivity filter, and that K+ selectivity is an intrinsic property of the filter. We hypothesize that the equilibrium preference for K+ ions originates in part through the optimal spacing between sites to accommodate multiple K+ ions within the selectivity filter.
Collapse
Affiliation(s)
- Shian Liu
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | | |
Collapse
|
11
|
Abstract
Thermodynamic measurements of ion binding to the Streptomyces lividans K(+) channel were carried out using isothermal titration calorimetry, whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography. Here we use these assays to show that the ion radius dependence of selectivity stems from the channel's recognition of ion size (i.e., volume) rather than charge density. Ion size recognition is a function of the channel's ability to adopt a very specific conductive structure with larger ions (K(+), Rb(+), Cs(+), and Ba(2+)) bound and not with smaller ions (Na(+), Mg(2+), and Ca(2+)). The formation of the conductive structure involves selectivity filter atoms that are in direct contact with bound ions as well as protein atoms surrounding the selectivity filter up to a distance of 15 A from the ions. We conclude that ion selectivity in a K(+) channel is a property of size-matched ion binding sites created by the protein structure.
Collapse
Affiliation(s)
- Steve W Lockless
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Ming Zhou
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| |
Collapse
|
12
|
Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R. Evolutionary information for specifying a protein fold. Nature 2005; 437:512-8. [PMID: 16177782 DOI: 10.1038/nature03991] [Citation(s) in RCA: 287] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Accepted: 06/30/2005] [Indexed: 11/08/2022]
Abstract
Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures. The artificial proteins show thermodynamic stabilities similar to natural WW domains, and structure determination of one artificial protein shows excellent agreement with the WW fold at atomic resolution. The relative simplicity of the information used for creating sequences suggests a marked reduction to the potential complexity of the protein-folding problem.
Collapse
Affiliation(s)
- Michael Socolich
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
| | | | | | | | | | | |
Collapse
|
13
|
Vergani P, Lockless SW, Nairn AC, Gadsby DC. CFTR channel opening by ATP-driven tight dimerization of its nucleotide-binding domains. Nature 2005; 433:876-80. [PMID: 15729345 PMCID: PMC2756053 DOI: 10.1038/nature03313] [Citation(s) in RCA: 336] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Accepted: 12/22/2004] [Indexed: 11/08/2022]
Abstract
ABC (ATP-binding cassette) proteins constitute a large family of membrane proteins that actively transport a broad range of substrates. Cystic fibrosis transmembrane conductance regulator (CFTR), the protein dysfunctional in cystic fibrosis, is unique among ABC proteins in that its transmembrane domains comprise an ion channel. Opening and closing of the pore have been linked to ATP binding and hydrolysis at CFTR's two nucleotide-binding domains, NBD1 and NBD2 (see, for example, refs 1, 2). Isolated NBDs of prokaryotic ABC proteins dimerize upon binding ATP, and hydrolysis of the ATP causes dimer dissociation. Here, using single-channel recording methods on intact CFTR molecules, we directly follow opening and closing of the channel gates, and relate these occurrences to ATP-mediated events in the NBDs. We find that energetic coupling between two CFTR residues, expected to lie on opposite sides of its predicted NBD1-NBD2 dimer interface, changes in concert with channel gating status. The two monitored side chains are independent of each other in closed channels but become coupled as the channels open. The results directly link ATP-driven tight dimerization of CFTR's cytoplasmic nucleotide-binding domains to opening of the ion channel in the transmembrane domains. This establishes a molecular mechanism, involving dynamic restructuring of the NBD dimer interface, that is probably common to all members of the ABC protein superfamily.
Collapse
Affiliation(s)
- Paola Vergani
- Laboratory of Cardiac/Membrane Physiology, The Rockefeller University, New York, New York 10021, USA.
| | | | | | | |
Collapse
|
14
|
Abstract
Members of the G protein superfamily contain nucleotide-dependent switches that dictate the specificity of their interactions with binding partners. Using a sequence-based method termed statistical coupling analysis (SCA), we have attempted to identify the allosteric core of these proteins, the network of amino acid residues that couples the domains responsible for nucleotide binding and protein-protein interactions. One-third of the 38 residues identified by SCA were mutated in the G protein Gs alpha, and the interactions of guanosine 5'-3-O-(thio)triphosphate- and GDP-bound mutant proteins were tested with both adenylyl cyclase (preferential binding to GTP-Gs alpha) and the G protein beta gamma subunit complex (preferential binding to GDP-Gs alpha). A two-state allosteric model predicts that mutation of residues that control the equilibrium between GDP- and GTP-bound conformations of the protein will cause the ratio of affinities of these species for adenylyl cyclase and G beta gamma to vary in a reciprocal fashion. Observed results were consistent with this prediction. The network of residues identified by the SCA appears to comprise a core allosteric mechanism conferring nucleotide-dependent switching; the specific features of different G protein family members are built on this core.
Collapse
Affiliation(s)
- Mark E Hatley
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA
| | | | | | | | | |
Collapse
|
15
|
Süel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003; 10:59-69. [PMID: 12483203 DOI: 10.1038/nsb881] [Citation(s) in RCA: 630] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Accepted: 11/19/2002] [Indexed: 11/09/2022]
Abstract
A fundamental goal in cellular signaling is to understand allosteric communication, the process by which signals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Here, we describe a sequence-based statistical method for quantitatively mapping the global network of amino acid interactions in a protein. Application of this method for three structurally and functionally distinct protein families (G protein-coupled receptors, the chymotrypsin class of serine proteases and hemoglobins) reveals a surprisingly simple architecture for amino acid interactions in each protein family: a small subset of residues forms physically connected networks that link distant functional sites in the tertiary structure. Although small in number, residues comprising the network show excellent correlation with the large body of mechanistic data available for each family. The data suggest that evolutionarily conserved sparse networks of amino acid interactions represent structural motifs for allosteric communication in proteins.
Collapse
Affiliation(s)
- Gürol M Süel
- Howard Hughes Medical Institute and Department of Pharmacology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
| | | | | | | |
Collapse
|
16
|
Abstract
For mapping energetic interactions in proteins, a technique was developed that uses evolutionary data for a protein family to measure statistical interactions between amino acid positions. For the PDZ domain family, this analysis predicted a set of energetically coupled positions for a binding site residue that includes unexpected long-range interactions. Mutational studies confirm these predictions, demonstrating that the statistical energy function is a good indicator of thermodynamic coupling in proteins. Sets of interacting residues form connected pathways through the protein fold that may be the basis for efficient energy conduction within proteins.
Collapse
Affiliation(s)
- S W Lockless
- Howard Hughes Medical Institute and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235-9050, USA
| | | |
Collapse
|
17
|
Lockless SW, Cheng HT, Hodel AE, Quiocho FA, Gershon PD. Recognition of capped RNA substrates by VP39, the vaccinia virus-encoded mRNA cap-specific 2'-O-methyltransferase. Biochemistry 1998; 37:8564-74. [PMID: 9622508 DOI: 10.1021/bi980178m] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have investigated the interaction of VP39, the vaccinia-encoded mRNA cap-specific 2'-O-methyltransferase, with its capped RNA substrate. Two sites on the protein surface, responsible for binding the terminal cap nucleotide (m7G) and cap-proximal RNA, were characterized, and a third (downstream RNA binding) site was identified. Regarding the crystallographically defined m7G binding pocket, VP39 showed significant activity with adenine-capped RNA. Although VP39 mutants lacking specific m7G-contact side chains within the pocket showed reduced catalytic activity, none was transformed into a cap-independent RNA methyltransferase. Moreover, each retained a preference for m7G and A over unmethylated G as the terminal cap nucleotide, indicating a redundancy of m7G-contact residues able to confer cap-type specificity. Despite containing the 2'-O-methylation site, m7GpppG (cap dinucleotide) could not be methylated by VP39, but m7GpppGUbiotinp could. This indicated the minimum-length 2'-O-methyltransferase substrate to be either m7GpppGp, m7GpppGpN, or m7GpppGpNp. RNA-protein contacts immediately downstream of the m7GpppG moiety were found to be pH-sensitive. This was detectable only in the context of a weakened interaction of near-minimum-length substrates with VP39's m7G binding pocket (through the use of either adenine-capped substrate or a VP39 pocket mutant), as a dramatic elevation of KM at pH values above 7.5. KM values for substrates with RNA chain lengths of 2-6 nt were between 160 and 230 nM, but dropped to 9-15 nM upon increasing chain lengths to 20-50 nt. This suggested the binding of regions of the RNA substrate >6 nt from the 5' terminus to a previously unknown site on the VP39 surface.
Collapse
Affiliation(s)
- S W Lockless
- Department of Biochemistry and Biophysics, Institute of Biosciences and Technology, Texas A&M University, Houston 77030, USA
| | | | | | | | | |
Collapse
|