Newsletter 536 (August
4, 2025) NIH Structural Biology Methods SIG
JULY 2025 PUBLICATIONS BY MEMBERS OF
THE GROUP
1: Liu C, Wu K, Choi H, Han HL, Zhang X, Watson JL, Ahn G,
Zhang JZ, Shijo S, Good LL, Fischer CM, Bera AK, Kang A, Brackenbrough E,
Coventry B, Hick DR, Qamar S, Li X, Decarreau J, Gerben SR, Yang W, Goreshnik
I, Vafeados D, Wang X, Lamb M, Murray A, Kenny S, Bauer MS, Hoofnagle AN, Zhu
P, Knowles TPJ, Baker D.
Diffusing
protein binders to intrinsically disordered proteins.
Nature 2025-07-31 doi: 10.1038/s41586-025-09248-9 PMID:
40739343
2: Chen X, Yao L, Li W, Ma S, Yuan X, Yang Y, Yuan Y, Liu
Y, Liu L, Wang H, Gellert M, Yang W.
How
RAG1/2 evolved from ancestral transposases to initiate V(D)J recombination
without transposition.
Proceedings of the National Academy of Sciences of the
United States of America 2025-07-29 doi: 10.1073/pnas.2512362122 PMID: 40729386
3: Sasse A, Ray D, Laverty KU, Tam CL, Albu M, Zheng H,
Levdansky Y, Lyudovyk O, Dalal T, Nie K, Magis C, Notredame C, Valkov E,
Weirauch MT, Hughes TR, Morris Q.
A
resource of RNA-binding protein motifs across eukaryotes reveals evolutionary
dynamics and gene-regulatory function.
Nature biotechnology 2025-07-28 doi:
10.1038/s41587-025-02733-6 PMID: 40715457
4: Gordon J, Kaminski AM, Bommu SR, Skrajna A, Petrovich
RM, Pedersen LC, McGinty RK, Warren AJ, Stanley RE.
PELP1
coordinates the modular assembly and enzymatic activity of the rixosome
complex.
Science advances 2025-07-25 doi: 10.1126/sciadv.adw4603
PMID: 40712028
5: Terayama K, Furuzono S, Fer N, Yan W, Young LC, Czyzyk
DJ, Goldstein de Salazar R, Sasaki M, Uozumi A, Konishi M, Kanda S, Sogawa Y,
Yamaguchi M, Tsuji T, Kuroyanagi J, Hayashi M, Ogura Y, Simanshu DK, Kubota K,
Tanaka J, McCormick F.
Molecular
glues that facilitate RAS binding to PI3Kα promote glucose uptake without
insulin.
Science (New York, N.Y.) 2025-07-24 doi:
10.1126/science.adr9097 PMID: 40705882
6: Zhao XZ, Wang W, Suazo KF, Al Mahmud MR, Agama K,
Lountos GT, Andresson T, Pommier Y, Burke TR.
Potent
Β-lactam-based tyrosyl-DNA phosphodiesterase 1 inhibitors identified by a
virtual screen.
Scientific reports 2025-07-22 doi:
10.1038/s41598-025-12503-8 PMID: 40691706
7: Sears AJ, Wild SH, Mesa-Eguiagaray I, Hall PS, Figueroa
JD.
Breast
cancer survival and mortality among women with type 2 diabetes: a retrospective
cohort study.
Scientific reports 2025-07-19 doi:
10.1038/s41598-025-08785-7 PMID: 40681529
8: Reveiz M, Tripathi P, Da Silva Pereira L, Kiyuka PK, Liu
T, Yang Y, Zhang B, Benmohamed D, Bonilla BG, Carruthers CW, Dillon M, Gowetski
D, Kratochvil S, Lagos G, Lofgren M, Loukinov I, Mathis-Torres S, Schaub AJ,
Scheideman E, Schön A, Shen CH, Flores-Garcia Y, Zavala F, Batista FD, Idris
AH, Seder RA, Kwong PD, Rawi R.
In
silico improvement of affinity for highly protective anti-malarial antibodies.
Science 2025-07-18 doi: 10.1016/j.isci.2025.112903 PMID:
40678545
9: Levdansky Y, Deme JC, Turner DJ, Piczak CT, Pekovic F,
Valkov AL, Tarasov SG, Lea SM, Valkov E.
Intracellular
pathogen effector reprograms host gene expression by inhibiting mRNA decay.
Nature communications 2025-07-13 doi:
10.1038/s41467-025-61194-2 PMID: 40651939
10: Le Cornet C, Jung AY, Behrens S, Middha P, Truong T,
Jernström H, Bolla MK, Wang Q, Southey MC, Beane Freeman LE, Koutros S, Stone
J, Rennert G, Shulman K, Aronson KJ, Murphy RA, Guénel P, Patel AV, Bodelon C,
Teras LR, Shahi S, Lacey JV, Dossus L, Kaaks R, Holleczek B, Brenner H, Brauch
H, Hoppe R, Czene K, Hall PFL, Mannermaa A, Wu AH, Obi N, Michailidou K,
Panayiotidis MI, McLean C, Haiman CA, Augustinsson A, Zheng W, Shu XO, Perou
CM, Troester MA, Van Alsten S, Eliassen AH, Abubakar M, Kraft P, Ahearn TU,
Evans DG, Wolk A, Milne RL, Easton DF, Pharoah PDP, Schmidt MK, García-Closas
M, Vachon CM, Fortner RT, Chang-Claude J.
Exogenous
Hormones, Tumor Intrinsic Subtypes, and Breast Cancer.
JAMA network open 2025-07-07 doi:
10.1001/jamanetworkopen.2025.19236 PMID: 40622713
11: Van CTS, Reboul CF, Caesar JJE, Meana-Pañeda R, Lountos
GT, Deme JC, Bryant OJ, Johnson S, Piczak CT, Valkov E, Lea SM, Elmlund H.
Probabilistic
single-particle cryo-EM ab initio 3D reconstruction in SIMPLE.
Acta crystallographica. Section D, Structural biology
2025-07-07 doi: 10.1107/S2059798325005686 PMID: 40622679
12: Celia H, Botos I, Ghirlando R, Duché D, Beach BM,
Lloubes R, Buchanan SK.
Cryo-EM
structures of the E. coli Ton and Tol motor complexes.
Nature communications 2025-07-02 doi:
10.1038/s41467-025-61286-z PMID: 40595649
13: Hassan B, Chandravanshi M, Ng MY, Negi H, Wilson BAP,
Walters KJ.
An
adaptive peptide-binding site in ubiquitin receptor hRpn13 revealed by
structural studies.
Nature communications 2025-07-02 doi:
10.1038/s41467-025-60843-w PMID: 40595513
14: Skorupka KA, Matsuoka K, Hassan B, Ghirlando R,
Balachandran V, Chen TH, Walters KJ, Schiffer CA, Wolf M, Iwatani Y, Matsuo H.
HIV-1
vif mediates ubiquitination of the proximal protomer in the APOBEC3H dimer to
induce degradation.
Nature communications 2025-07-02 doi:
10.1038/s41467-025-60984-y PMID: 40593686
15: Simanshu DK, Xu R, Stice JP, Czyzyk DJ, Feng S, Denson
JP, Riegler E, Yang Y, Zhang C, Donovan S, Smith BP, Abreu-Blanco M, Chen M,
Feng C, Fu L, Rabara D, Young LC, Dyba M, Yan W, Lin K, Ghorbanpoorvalukolaie
S, Larsen EK, Malik W, Champagne A, Parker K, Ju JH, Jeknic S, Esposito D,
Turner DM, Lightstone FC, Wang B, Wehn PM, Wang K, Stephen AG, Maciag AE, Hata
AN, Sinkevicius KW, Nissley DV, Wallace EM, McCormick F, Beltran PJ.
BBO-10203
inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3Kα
interaction.
Science (New York, N.Y.) 2025-06-12 doi:
10.1126/science.adq2004 PMID: 40504949
16: Witt KC, Dziulko A, An J, Pekovic F, Cheng AX, Liu GY,
Lee OV, Turner DJ, Lari A, Gaidt MM, Chavez R, Fattinger SA, Abraham P,
Dhaliwal H, Lee AY, Kotov DI, Coscoy L, Glaunsinger BA, Valkov E, Chuong EB,
Vance RE.
SP140-RESIST
pathway regulates interferon mRNA stability and antiviral immunity.
Nature 2025-06-12 doi: 10.1038/s41586-025-09152-2 PMID:
40500448
17: Liu L, Li J, Cisneros-Aguirre M, Merkell A, Stark JM,
Gellert M, Yang W.
Dynamic
assemblies and coordinated reactions of non-homologous end joining.
Nature 2025-06-12 doi: 10.1038/s41586-025-09078-9 PMID:
40500445
18: Alexander P, Chan AH, Rabara D, Swain M, Larsen EK,
Dyba M, Chertov O, Ashraf M, Champagne A, Lin K, Maciag A, Gillette WK, Nissley
DV, McCormick F, Simanshu DK, Stephen AG.
Biophysical
and structural analysis of KRAS switch-II pocket inhibitors reveals
allele-specific binding constraints.
The Journal of biological chemistry 2025-06-06 doi:
10.1016/j.jbc.2025.110331 PMID: 40473215
19: Maloney SM, Shaw TM, Nennig KM, Larsen MS, Shah A,
Kumar A, Marcotrigiano J, Grove J, Snijder EJ, Kirchdoerfer RN, Bailey AL.
CD81
is a receptor for equine arteritis virus (family:
mBio 2025-05-27 doi: 10.1128/mbio.00623-25 PMID: 40422661
20: Wu RL, Houser KV, Gaudinski MR, Widge AT, Awan SF,
Carter CA, Holman LA, Saunders J, Hendel CS, Eshun A, Whalen WR, Wang X, Arthur
A, Cunningham JE, Beck A, Casazza JP, Yamshchikov GV, Rothwell RS, Strom L,
Dittakavi T, Happe M, Hickman SP, Conan-Cibotti M, Carlton K, Zhang L, Huang Y,
Capparelli EV, Castro M, Lin BC, O'Connell S, Flach BS, Bailer RT, Narpala SR,
Serebryannyy L, McDermott AB, Arnold FJ, Gall JG, Vazquez S, Berkowitz NM,
Gordon IJ, Chen GL, Kwong PD, Huang J, Pierson TC, Connors M, Mascola JR, Zhou
T, Doria-Rose NA, Koup RA, Dropulic LK, None None.
Safety
and pharmacokinetics of N6LS, a broadly neutralising monoclonal antibody for
HIV: a phase 1, open-label, dose-escalation study in healthy adults.
The lancet. HIV 2025-05-24 doi:
10.1016/S2352-3018(25)00041-4 PMID: 40409326
21: Wang'ondu RW, Ashcraft E, Chang TC, Roberts KG, Brady
SW, Fan Y, Evans W, Relling MV, Crews KR, Yang J, Yang W, Pounds S, Wu G,
Devidas M, Maloney K, Mattano L, Schore RJ, Angiolillo A, Larsen E, Salzer W,
Burke MJ, Loh ML, Jeha S, Pui CH, Inaba H, Cheng C, Mullighan CG.
Heterogeneity
of IKZF1 genomic alterations and risk of relapse in childhood B-cell precursor
acute lymphoblastic leukemia.
Leukemia 2025-05-14 doi: 10.1038/s41375-025-02633-3 PMID:
40360879
22: Buchsbaum JC, VanBrocklin HF, Hernandez R, O'Brien EM,
Hennkens HM, Medvedev DG, Howell RW, Escorcia FE, Dewaraja YK, Jha AK, Kapadia
AJ, Agasthya G, Rahmim A, Saboury B, Myhre K, Davern S.
Computational
Modeling to Advance Novel Medical Isotopes for Radiotheranostics: A DOE-NIH
Joint Workshop Executive Summary.
Radiation research 2025-05-02 doi: 10.1667/RADE-25-00MR1.1
PMID: 40314593
23: Fullenkamp CR, Mehdi S, Jones CP, Tenney L, Pichling P,
Prestwood PR, Ferré-D'Amaré AR, Tiwary P, Schneekloth JS.
Machine
Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the
Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.
Angewandte Chemie (International ed. in English) 2025-05-01
doi: 10.1002/anie.202505971 PMID: 40310613
RECENT
TOPICS IN THE LITERATURE:
METHODS
— Sample Preparation Tips
N. Premaraj et al., "Advancing
cryo-EM and cryo-ET through innovation in sample carriers: a perspective" PMID:
40476672.
I.J. Hirst et al., "Untangling
the effects of flexibility and the AWI in cryoEM sample preparation: A case
study using KtrA" PMID: 40324569.
Y. Huang et al., "Recent
Advances in Expression Screening and Sample Evaluation for Structural Studies
of Membrane Proteins" PMID: 39362625.
K. McGuire et al., "Tuning
ice thickness using the chameleon for high-quality cryoEM data collection" PMID:
38746094.
B. Cook et al., "Preparation
of oxygen-sensitive proteins for high-resolution cryoEM structure determination
using (an)aerobic blot-free vitrification" PMID: 39091810.
R. Warmack et al., "Anaerobic
cryoEM protocols for air- sensitive nitrogenase proteins" PMID:
38575747.
I.J. Hirst et al., "CryoEM
grid preparation: a closer look at advancements and impact of preparation mode
and new approaches" PMID: 38864435.
S. Yadav and K.R. Vinothkumar, "Factors
affecting macromolecule orientations in thin films formed in cryo-EM" PMID:
38935342.
S.E.J. Bowman et al., "Preparing
research samples for safe arrival at centers and facilities: recipes for
successful experiments" PMID: 38990054.
METHODS
— Macromolecular Crystallography
N. L. Inniss et al., "Structural
genomics of bacterial drug targets: application of a high-throughput pipeline
to solve 59 protein structures from pathogenic and related bacteria" PMID:
40391899.
.J. Simpkin et al. "Slice'N'Dice:
maximizing the value of predicted models for structural biologists" PMID:
39976565.
G. Budziszewski et al. "Preparing
for successful protein crystallization experiments" PMID:
40454464.
M. Schaefer et al., "Surface-mutagenesis
strategies to enable structural biology crystallization platforms" PMID:
39207897.
METHODS
— Integrative Structural Biology
S. Bazzi and S. Sayyed, "Revealing
arginine-cysteine and glycine-cysteine NOS linkages by a systematic
re-evaluation of protein structures" PMID: 40360719.
R. Mitra et al. "RNAproDB:
a webserver and interactive database for analyzing protein-RNA
interactions" PMID: 40126909.
H. McCann et al., "R2DT:
a comprehensive platform for visualizing RNA secondary structure" PMID:
39921562.
B. Vallat et al., "PDB-IHM:
a system for deposition, curation, validation, and dissemination of integrative
structures" PMID: 40110969.
D. A. Erlanson et al., "Where
and how to house big data on small fragments" PMID:
40325009.
M. Bazayeva et al., "A
database overview of metal-coordination distances in metalloproteins" PMID:
38682667.
H. Zheng et al., "PinMyMetal:
a hybrid learning system to accurately model metal binding sites in
macromolecules" PMID: 40155596.
M. Bochtler, "X-rays,
electrons, and neutrons as probes of atomic matter" PMID:
38412856.
METHODS
— XFEL, Serial Crystallography
L. Sauthof et al. "Serial-femtosecond
crystallography reveals how a phytochrome variant couples chromophore and
protein structural changes" PMID: 40435264.
M. Maestre-Reyna et al., "Capturing
structural intermediates in an animal-like cryptochrome photoreceptor by
time-resolved crystallography" PMID: 40378212.
M. Sonawal et al. "Functional
implications of hexameric dynamics in SARS-CoV-2 Nsp15" PMID:
40411374.
METHODS
— Micro-ED
M.T.B. Clabbers and T. Gonen, "Recovering
high-resolution information using energy filtering in MicroED" PMID:
40370641.
J. Lin et al., "Ligand
screening and discovery using cocktail soaking and automated MicroED" PMID:
40027750.
W. J. Nicolas et al., "Structure
of the lens MP20 mediated adhesive junction" PMID:
40140346.
J.E. Miller et al., "AlphaFold-assisted
structure determination of a bacterial protein of unknown function using X-ray
and electron crystallography" PMID: 38451205.
METHODS
— Cryo-EM
R.C. Kretsch et al., "Complex
water networks visualized by cryogenic electron microscopy of RNA" PMID:
40068818.
R.C. Kretsch et al., "Naturally
ornate RNA-only complexes revealed by cryo-EM" PMID:
40328315.
G. Pintilie et al., "Q-score
as a reliability measure for protein, nucleic acid, and small molecule atomic
coordinate models derived from 3DEM density maps" PMID:
39868161.
R. Read et al., "Likelihood-based
interactive local docking into cryo-EM maps in ChimeraX" PMID:
39058381.
R. Karimi et al., "Vesicle
Picker: a tool for efficient identification of membrane protein complexes in
vesicles" PMID: 39481498.
D. Bobe et al., "Multi-species
cryoEM calibration and workflow verification standard" PMID:
39494502.
C.L. Lawson et al., "Outcomes
of the EMDataResource Cryo-EM Ligand Modeling Challenge" PMID:
38343795.
B. Greber et al., "High-resolution
cryo-EM of the human CDK-activating kinase for structure-based drug
design" PMID: 38480681.
G.J. Kleywegt, "Community
recommendations on cryoEM data archiving and validation" PMID:
38358351.
M. Kschonsak et al., "Cryo-EM
reveals an unprecedented binding site for Nav1.7 inhibitors enabling rational
design of potent hybrid inhibitors" PMID: 36975198.
METHODS
— SAXS
E. Brookes et al., "SAXS-A-Fold:
a website for fast ensemble modeling optimizing the fit of AlphaFold or
user-supplied protein structures with flexible regions to SAXS data" PMID:
40475948.
K. Lytje and J.S. Pederson, "Validation
of electron-microscopy maps using solution small-angle X-ray scattering" PMID:
38935344.
METHODS
— NMR Spectroscopy
L. S. Pidgu et al., "Observing
nucleotide flipping in DNA using indirect 2’-F nucleotide probes and 19F
NMR" PMID: 40488280.
M. Bütikofer et al., "Rapid
Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR" PMID:
38957136.
METHODS
— AlphaFold
A. Fadini et al., "AlphaFold
as a prior: experimental structure determination conditioned on a pretrained
neural network" PMID: 40027838.
R.M. Keegan et al., "The
success rate of processed predicted models in molecular replacement:
implication for experimental phasing in the AlphaFold era" PMID:
39360967.
B.K. Poon et al., "The
Phenix-AlphaFold webservice: enabling AlphaFold predictions for use in
Phenix" PMID: 3864706.
A.M. Lau et al., "Exploring
structural diversity across the protein universe with The Encyclopedia of
Domains" PMID: 39480926.
J. Abramson et al., "Accurate
structure prediction of biomolecular interactions with AlphaFold 3" PMID:
38718835.
METHODS
— Mass Spectrometry
M.A. Gonzalez-Lozano et al., "EndoMAP.v1
charts the structural landscape of human early endosome complexes" PMID:
40437099.
R.A. D'Ippoito et al., "Determining
KRAS4B-Targeting Compound Specificity by Top-Down Mass Spectrometry" PMID:
39052227.
A. Vetrano et al., "Protein
secondary structure patterns in short-range cross-link atlas" PMID:
4043759.
M.D. Mann et al., "Structural
proteomics defines a sequential priming mechanism for the progesterone
receptor" PMID: 403555435.
READINGS
& TUTORIALS — General Structural Biology
R. Nussinov et al., "Allostery
in disease: anticancer drugs, pockets, and the tumor heterogeneity
challenge" PMID: 40021049.
K. Matange et al., "Biological
polymers: evolution, function, and significance" PMID:
39905926.
L.C. Schofield et al., "Post-translational
modifications in the Protein Data Bank" PMID: 39207896.
READINGS
& TUTORIALS — Macromolecular Crystallography
K.L. Shelley and E.F. Garman, "Identifying
and avoiding radiation damage in macromolecular crystallography" PMID:
38700059.
G. Khusainov et al., "The
time revolution in macromolecular crystallography" PMID:
38616866.
J.R. Helliwell et al., "The
evolution of raw data archiving and the growth of its importance in
crystallography" PMID: 38864497.
D.J. Haas, "Fifty years on: why macromolecular
cryocrystallography has been so successful" IUCr Newsletter (2023) 31(3).
W.A. Hendrickson, "Facing
the phase problem" PMID: 37668214.
READINGS
& TUTORIALS — Cryo-EM
C.T. Chien et al., "Single-particle
cryogenic electron microscopy structure determination for membrane
proteins" PMID: 40228430.
G.C. Lander, "Single
particle cryo-EM map and model validation: It's not crystal clear" PMID:
39293191.
E. Nogales & J. Mahamid, "Bridging
structural and cell biology with cryo-electron microscopy" PMID:
38570716.
READINGS
& TUTORIALS — Serial Crystallography
C. J. Tremlett et al., "Small
but mighty: the power of microcrystals in structural biology" PMID:
40080159.
A. Henkel and D. Oberthur, "A
snapshot love story: what serial crystallography has done for us" PMID:
38984902.
READINGS
& TUTORIALS — MicroED
A. Haymaker & B.L. Nannenga, "Advances
and applications of microcrystal electron diffraction (MicroED)" PMID:
10882645.
READINGS
& TUTORIALS — NMR Spectroscopy
O. A. Alimowska et al., "Advances
in the application of NMR to the study of GPCRs and ligand-GPCR
interactions" PMID: 40485639.
G. Platzer et al., "NMR-driven
structure-based drug discovery by unveiling molecular interactions" PMID:
40450181.
READINGS
& TUTORIALS — Atomic Force Microscopy (AFM)
Y. Jiang et al., "A
structural biology compatible file format for atomic force microscopy" PMID:
39955301.
A.C. Dumitru et al., "Recent
advances in the application of atomic force microscopy to structural
biology" PMID: 37044358.
READINGS
& TUTORIALS — AlphaFold/AI
E. Callaway, "Chemistry
Nobel goes to developers of AlphaFold AI that predicts protein structures" PMID:
39384918.
E. Callaway, "The
huge protein database that spawned AlphaFold and biology's AI revolution" PMID:
39424937.
T.C. Terwilliger et al., "AlphaFold
predictions are valuable hypotheses and accelerate but do not replace
experimental structure determination" PMID: 38036854.
S. Subramaniam, "Structural
biology in the age of AI" PMID: 38066345.
READINGS
& TUTORIALS — Protein Data Bank/Data Archiving
H. Berman and S.K. Burley, "Protein
Data Bank (PDB): Fifty-three years young and having a transformative impact on
science and society" PMID: 39973356.
S.K. Burley et al., "Updated
resources for exploring experimentally-determined PDB structures and computed
structure models at the RCSB Protein Data Bank" PMID:
39607707.
IN THE
NEWS:
Ruth Nussinov elected to the National Academy of
Sciences, 05/02/2025
Simulations implicate structural changes as a culprit in
mutant protein’s cancer role and point to possible treatments, 03/25/2025
Lipoprotein structure gives insights into "bad"
cholesterol, 01/14/2025
DATABASES
— Structural Biology
AlphaFold DB
BioCyc
DisProt
ExPASy
HAD
HIC-Up
NDB
PDB
PDBe
PDB SARS-CoV-2 Resources
SARS-CoV-2
Related Structures
RaMP-DB
virusMED